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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

LSST Undergraduate Internships at Fermilab

Fermi National Accelerator Laboratory (Fermilab) plans to leverage the laboratory’s long tradition of hosting internships in high-energy physics and cosmology by setting up a mentoring laboratory program for undergraduate students to study data and model driven Large Synoptic Survey Telescope (LSST) science at the laboratory’s Center for Particle Astrophysics. The laboratory program will form an intern group that will explore the science of combining of LSST analysis using DC2 simulations and CosmoSIS modeling. Interns will be empowered to learn from each other while under the supervision of experienced cosmic frontier scientists, a model that has been successful in the laboratory setting. In addition, many of these undergraduate interns will form future candidate graduate student classes

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

JWST Noise Floor. I. Random Error Sources in JWST NIRCam Time Series

James Webb Space Telescope (JWST) transmission and emission spectra will provide invaluable glimpses of transiting exoplanet atmospheres, including possible biosignatures. This promising science from JWST, however, will require exquisite precision and understanding of systematic errors that can impact the time series of planets crossing in front of and behind their host stars. Here, we provide estimates of the random noise sources affecting JWST Near-Infrared Camera (NIRCam) time-series data on the integration-to-integration level. We find that 1/f noise can limit the precision of grism time series for two groups (230–1000 ppm depending on the extraction method and extraction parameters), but will average down like the square root of N frames/reads. The current NIRCam grism time-series mode is especially affected by 1/f noise because its GRISMR dispersion direction is parallel to the detector fast-read direction, but could be alleviated in the GRISMC direction. Care should be taken to include as many frames as possible per visit to reduce this 1/f noise source: thus, we recommend the smallest detector subarray sizes one can tolerate, four output channels, and readout modes that minimize the number of skipped frames (RAPID or BRIGHT2). We also describe a covariance-weighting scheme that can significantly lower the contributions from 1/f noise as compared to sum extraction. We evaluate the noise introduced by pre-amplifier offsets, random telegraph noise, and high dark current resistor capacitor (RC) pixels and find that these are correctable below 10 ppm once background subtraction and pixel masking are performed. We explore systematic error sources in a companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Expediting DECam Multimessenger Counterpart Searches with Convolutional Neural Networks

Searches for counterparts to multimessenger events with optical imagers use difference imaging to detect new transient sources. However, even with existing artifact-detection algorithms, this process simultaneously returns several classes of false positives: false detections from poor-quality image subtractions, false detections from low signal-to-noise images, and detections of preexisting variable sources. Currently, human visual inspection to remove the false positives is a central part of multimessenger follow-up observations, but when next generation gravitational wave and neutrino detectors come online and increase the rate of multimessenger events, the visual inspection process will be prohibitively expensive. We approach this problem with two convolutional neural networks operating on the difference imaging outputs. The first network focuses on removing false detections and demonstrates an accuracy of 92% on our data set. The second network focuses on sorting all real detections by the probability of being a transient source within a host galaxy and distinguishes between various classes of images that previously required additional human inspection. We find the number of images requiring human inspection will decrease by a factor of 1.5 using our approach alone and a factor of 3.6 using our approach in combination with existing algorithms, facilitating rapid multimessenger counterpart identification by the astronomical community.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Alignments in the orientation of radio jets from AGN and their host galaxies

It is well established that active galactic nuclei (AGNs) play an important role in the evolution of galaxies. These AGNs can be linked to the accretion processes onto massive black holes and past merger events in their host galaxies, which may lead to different alignments of the jets with respect to the host galaxies. This paper presents a study of the position angle (PA) differences between radio and optical images of radio-AGNs based on the second data release (DR2) of the Low Frequency Array (LOFAR) Two-Meter Sky Survey (LoTSS), theKarl G. JanskyVery Large Array Faint Images of the Radio Sky at Twenty-Centimeters Survey (FIRST), the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys, and the Sloan Digital Sky Survey (SDSS). We assessed PA measurement biases in the data and classified the radio-AGNs based on the radio luminosity and infrared colour from the Wide-field Infrared Survey Explorer (WISE). This resulted in the largest sample of radio AGNs with reliable radio and optical PA measurements published to date, with a total of 3682 AGNs. The PA difference (dPA) distributions for the radio-AGN sample show a prominent minor-axis alignment tendency. Based on some simple assumptions, we simulated the projection effect to estimate the intrinsic jet-galaxy alignment. The observed dPA distribution can be well described by a two-component jet-alignment model in which one component is more aligned with the minor axis of the host galaxy than the other. The fitting results indicate that the jet alignment is dependent on radio luminosity and the shape of the host galaxies, with the jets being more likely to be aligned with the minor axis of the galaxy for lower radio luminosity and for optically more elongated radio-AGNs. The minor-axis alignment of the entire sample may suggest a coherent accretion model present in most AGN host galaxies, while a considerable number of luminous radio-AGNs with massive host galaxies might have undergone accretion – according to the chaotic model – or past merger events.

Astronomy & Astrophysics↗
DOE OSTI2021

Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods

Symbiotic relationships between heterotrophic and phototrophic partners are common in microbial eukaryotes. Among Arcellinida (Amoebozoa) several species are associated with microalgae of the genus Chlorella (Archaeplastida). So far, these symbioses were assumed to be stable and mutualistic, yet details of the interactions are limited. Here, we analyzed 22 single-cell transcriptomes and 36 partially-sequenced genomes of the Arcellinida morphospecies Hyalosphenia papilio, which contains Chlorella algae, to shed light on the amoeba-algae association. By characterizing the genetic diversity of associated Chlorella, we detected two distinct clades that can be linked to host genetic diversity, yet at the same time show a biogeographic signal across sampling sites. Fluorescence and transmission electron microscopy showed the presence of intact algae cells within the amoeba cell. Yet analysis of transcriptome data suggested that the algal nuclei are inactive, implying that instead of a stable, mutualistic relationship, the algae may be temporarily exploited for photosynthetic activity before being digested. Furthermore, differences in gene expression of H. papilio and Hyalosphenia elegans demonstrated increased expression of genes related to oxidative stress. Together, our analyses increase knowledge of this host-symbiont association and reveal 1) higher diversity of associated algae than previously characterized, 2) a transient association between H. papilio and Chlorella with unclear benefits for the algae, 3) algal-induced gene expression changes in the host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Coupled Mathematical Model of the Intracellular Replication of Dengue Virus and the Host Cell Immune Response to Infection

Dengue virus (DV) is a positive-strand RNA virus of the Flavivirus genus. It is one of the most prevalent mosquito-borne viruses, infecting globally 390 million individuals per year. The clinical spectrum of DV infection ranges from an asymptomatic course to severe complications such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS), the latter because of severe plasma leakage. Given that the outcome of infection is likely determined by the kinetics of viral replication and the antiviral host cell immune response (HIR) it is of importance to understand the interaction between these two parameters. In this study, we use mathematical modeling to characterize and understand the complex interplay between intracellular DV replication and the host cells' defense mechanisms. We first measured viral RNA, viral protein, and virus particle production in Huh7 cells, which exhibit a notoriously weak intrinsic antiviral response. Based on these measurements, we developed a detailed intracellular DV replication model. We then measured replication in IFN competent A549 cells and used this data to couple the replication model with a model describing IFN activation and production of IFN stimulated genes (ISGs), as well as their interplay with DV replication. By comparing the cell line specific DV replication, we found that host factors involved in replication complex formation and virus particle production are crucial for replication efficiency. Regarding possible modes of action of the HIR, our model fits suggest that the HIR mainly affects DV RNA translation initiation, cytosolic DV RNA degradation, and naïve cell infection. We further analyzed the potential of direct acting antiviral drugs targeting different processes of the DV lifecycle in silico and found that targeting RNA synthesis and virus assembly and release are the most promising anti-DV drug targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein—the primary target of global vaccine efforts—are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Optimization of X-ray event screening using ground and in-orbit data for the Resolve instrument onboard the XRISM satellite

The X-Ray Imaging and Spectroscopy Mission (XRISM) satellite was successfully launched and put into a low-Earth orbit on September 6, 2023 (UT). The Resolve instrument onboard XRISM hosts an X-ray microcalorimeter detector, which was designed to achieve a high-resolution ( ≤ 7 eV FWHM at 6 keV), high-throughput, and non-dispersive spectroscopy over a wide energy range. It also excels in a low background with a requirement of < 2 × 10 -3 s -1 keV -1 (0.3 to 12.0 keV), which is equivalent to only one background event per spectral bin per 100-ks exposure. Event screening to discriminate X-ray events from background is a key to meeting the requirement. We present the result of the Resolve event screening using data sets recorded on the ground and in orbit based on the heritage of the preceding X-ray microcalorimeter missions, in particular, the Soft X-ray Spectrometer onboard ASTRO-H. We optimize and evaluate 19 screening items of three types based on (1) the event pulse shape, (2) relative arrival times among multiple events, and (3) good time intervals. We show that the initial screening, which is applied for science data products in the performance verification phase, reduces the background rate to 1.8 × 10 -3 s -1 keV -1 meeting the requirement. We further evaluate the additional screening utilizing the correlation among some pulse shape properties of X-ray events and show that it further reduces the background rate, particularly in the < 2 keV band. Over 0.3 to 12 keV, the background rate becomes 1.0 × 10 -3 s -1 keV -1 .

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

SEM petrography of dispersed organic matter in black shales: A review

Organic matter (OM)-hosted pores are important constituents of the pore system of black shales and play a crucial role in determining their methane adsorption capacity and porosity. OM-hosted pores are generally observed and described with scanning electron microscope (SEM) on Ar ion-milled surfaces. However, SEM imaging is not able to reliably distinguish OM types and relate the observed pores to specific macerals. Partly because of this inability to relate organic pores to macerals, the evolution of organic porosity during thermal maturation remains poorly understood. In this paper, we review the petrographic characteristics of dispersed organic matter (DOM) in black shales under the SEM. Organic petrographic classification of DOM developed for reflected-light microscopy is so far the most practical method when describing DOM in black shales under the SEM because this classification has information on the origin of DOM. Therefore, correlative microscopy (combination of reflected-light and electron microscopy) is the most effective method to identify both OM types and OM-hosted pores. This method, however, is not readily available to most researchers. Although identifying OM on the basis of SEM observations is a challenging task, it is achievable provided there is a good understanding of the studied shales, especially their thermal maturity and original OM composition. Therefore, the overall objective of this paper is to review petrographic characteristics of DOM in black shales under the SEM to provide some guidelines for identifying DOM from SEM observations. We also review factors that control the formation and preservation of OM-hosted pores. OM-hosted pores consist of primary and secondary organic pores. Primary organic pores are pores inherited from the biological structure of the original OM. Secondary organic pores develop during hydrocarbon generation and expulsion from oil-prone OM and are hosted by solid bitumen or pyrobitumen. The development of secondary organic pores is controlled by thermal maturity and OM type, and their preservation is subject to thermal maturity, OM content, and mineralogical composition. The presented view of the evolution of micropore and mesopore characteristics of OM with thermal maturity is based on data from the literature. The specific surface area and pore volume of OM in black shales follow a parabolic pattern with increasing thermal maturity (quantified via vitrinite reflectance, R o ). The initial increase reflects development of OM-hosted pores, and the subsequent decrease is due to denser stacking of aromatic units in the macromolecular structure of OM, with maximum values (specific surface area ~ 300 m 2 /g and pore volume ~ 0.3 cm 3 /g) reached at R o values in the 2.5-3.5% range. The contribution of OM-hosted pores to the pore characteristics of black shales depends on OM content, OM type, and thermal maturity.

03 NATURAL GAS↗
DOE OSTI2023

PubDAS: A PUBlic Distributed Acoustic Sensing Datasets Repository for Geosciences

During the past few years, distributed acoustic sensing (DAS) has become an invaluable tool for recording high-fidelity seismic wavefields with great spatiotemporal resolutions. However, the considerable amount of data generated during DAS experiments limits their distribution with the broader scientific community. Such a bottleneck inherently slows down the pursuit of new scientific discoveries in geosciences. Here, we introduce PubDAS—the first large-scale open-source repository where several DAS datasets from multiple experiments are publicly shared. PubDAS currently hosts eight datasets covering a variety of geological settings (e.g., urban centers, underground mines, and seafloor), spanning from several days to several years, offering both continuous and triggered active source recordings, and totaling up to ~90 TB of data. Here this article describes these datasets, their metadata, and how to access and download them. Some of these datasets have only been shallowly explored, leaving the door open for new discoveries in Earth sciences and beyond.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Do Minor Interactions Trigger Star Formation in Galaxy Pairs?

Abstract We analyze the galaxy pairs in a set of volume limited samples from the Sloan Digital Sky Survey to study the effects of minor interactions on the star formation rate (SFR) and color of galaxies. We carefully design control samples of isolated galaxies by matching the stellar mass and redshift of the minor pairs. The SFR distributions and color distributions in the minor pairs differ from their controls at >99% significance level. We also simultaneously match the control galaxies in stellar mass, redshift and local density to assess the role of the environment. The null hypothesis can be rejected at >99% confidence level even after matching the environment. Our analysis shows a quenching in the minor pairs where the degree of quenching decreases with the increasing pair separation and plateaus beyond 50 kpc. We also prepare a sample of minor pairs with H α line information. We calculate the SFR of these galaxies using the H α line and repeat our analysis. We observe a quenching in the H α sample too. We find that the majority of the minor pairs are quiescent systems that could be quenched due to minor interactions. Combining data from the Galaxy Zoo and Galaxy Zoo 2, we find that only ∼1% galaxies have a dominant bulge, 4%–7% galaxies host a bar and 5%–10% of galaxies show active galactic nucleus (AGN) activity in minor pairs. This indicates that the presence of bulge, bar or AGN activity plays an insignificant role in quenching the galaxies in minor pairs. The more massive companion satisfies the criteria for mass quenching in most of the minor pairs. We propose that the stripping and starvation likely caused the quenching in the less massive companion at a later stage of evolution.

Astronomy & Astrophysics↗
DOE OSTI2022

MIGHTEE: the nature of the radio-loud AGN population

ABSTRACT We study the nature of the faint radio source population detected in the MeerKAT International GHz Tiered Extragalactic Exploration (MIGHTEE) Early Science data in the COSMOS field, focusing on the properties of the radio-loud active galactic nuclei (AGNs). Using the extensive multiwavelength data available in the field, we are able to classify 88 per cent of the 5223 radio sources in the field with host galaxy identifications as AGNs (35 per cent) or star-forming galaxies (54 per cent). We select a sample of radio-loud AGNs with redshifts out to z ∼ 6 and radio luminosities 1020 < L1.4 GHz/W Hz−1 < 1027 and classify them as high-excitation and low-excitation radio galaxies (HERGs and LERGs). The classification catalogue is released with this work. We find no significant difference in the host galaxy properties of the HERGs and LERGs in our sample. In contrast to previous work, we find that the HERGs and LERGs have very similar Eddington-scaled accretion rates; in particular we identify a population of very slowly accreting AGNs that are formally classified as HERGs at these low radio luminosities, where separating into HERGs and LERGs possibly becomes redundant. We investigate how black hole mass affects jet power, and find that a black hole mass ≳ 107.8 M⊙ is required to power a jet with mechanical power greater than the radiative luminosity of the AGN (Lmech/Lbol > 1). We discuss that both a high black hole mass and black hole spin may be necessary to launch and sustain a dominant radio jet.

Whittam, I. H. (ORCID:0000000322655983)↗
DOE OSTI2024

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Strong Superexchange in a $d^{9–δ}$ Nickelate Revealed by Resonant Inelastic X-Ray Scattering

The discovery of superconductivity in a $d^{9–δ}$ nickelate has inspired disparate theoretical perspectives regarding the essential physics of this class of materials. A key issue is the magnitude of the magnetic superexchange, which relates to whether cuprate-like high-temperature nickelate superconductivity could be realized. In this work, we address this question using Ni L-edge and O K-edge spectroscopy of the reduced $d^{9–1/3}$ trilayer nickelates R 4 Ni 3 O 8 (where R = La, Pr) and associated theoretical modeling. A magnon energy scale of ~80 meV resulting from a nearest-neighbor magnetic exchange of J = 69 (4) meV is observed, proving that $d^{9–δ}$ nickelates can host a large superexchange. This value, along with that of the Ni-O hybridization estimated from our O K-edge data, implies that trilayer nickelates represent an intermediate case between the infinite-layer nickelates and the cuprates. Layered nickelates thus provide a route to testing the relevance of superexchange to nickelate superconductivity.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Human Lung Fibroblast Response to HCoV-229E Infection, Top-down Proteomics of Histones (ACS-TZ-DP7)

The purpose of this experiment was to evaluate the human host cellular response to wild type human coronavirus strain 229E (HCoV-229E) infection, specifically how histones are modified following infection. Sample data was obtained from mock-infected and HCoV-229E-infected immortalized human lung fibroblasts (MRC-5) (MOI 3). Whole cell lysates were collected at 24 hours post infection and histones from all samples were enriched and were processed for proteoform identification analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Powered By SAM [Slides]

The System Advisor Model(TM) (SAM) is a free, open-source desktop application for techno-economic analysis of energy technologies. By combining detailed performance modeling with financial analysis, SAM allows users to assess technology trade-offs, explore future scenarios, and make informed decisions about energy investments. Users also have access to model details and the ability to embed SAM's core models in their own applications. This webinar, hosted by National Laboratory of the Rockies researchers Janine Keith and Matt Prilliman, highlights how this widely used modeling tool supports data-driven decision-making for energy systems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗