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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 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Infrastructure first principles for the Anthropocene

Abstract There appears to be a growing decoupling between the conditions that infrastructures were designed for and today’s rapidly changing environments. Infrastructures today are largely predicated on the technologies, goals, and governance structures from a century ago. While infrastructures continue to deliver untold value, there is growing evidence that these critical, basic, and lifeline systems appear ill-equipped to confront the volatility, uncertainty, accelerating conditions, and complexity that define them and their changing environments. Innovative and disruptive first principles are needed to guide infrastructures in the Anthropocene. Drawing from emerging infrastructure research and disciplines that appear better able to confront disruption and change, a novel set of first principles are identified: (1) Plan for complex conditions and surprise; (2) Recouple with agility and flexibility; (3) Govern for exploration and instability; (4) Build consensus as control decentralizes; (5) Restructure to engage with porous boundaries; and, (6) Cyberthreat planning is now mission critical. These principles should guide infrastructure planning recognizing the changing nature and increasingly obsolete boundaries that have defined engineered systems in the modern era.

Chester, Mikhail (ORCID:0000000293542102)↗
DOE OSTI2023

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction

TRIMER, Transcription Regulation Integrated with MEtabolic Regulation, is a genome-scale modeling pipeline targeting at metabolic engineering applications. Using TRIMER, regulated metabolic reactions can be effectively predicted by integrative modeling of metabolic reactions with a Transcription Factor (TF)-gene regulatory network (TRN), which is modeled via a Bayesian network (BN). In this paper, we focus on sensitivity analysis of metabolic flux prediction for uncertainty quantification of BN structures for TRN modeling in TRIMER. We propose a computational strategy to construct the uncertainty class of TRN models based on the inferred regulatory order uncertainty given transcriptomic expression data. With that, we analyze the prediction sensitivity of the TRIMER pipeline for the metabolite yields of interest. The obtained sensitivity analyses can guide Optimal Experimental Design (OED) to help acquire new data that can enhance TRN modeling and achieve specific metabolic engineering objectives, including metabolite yield alterations. Here we have performed small- and large-scale simulated experiments, demonstrating the effectiveness of our developed sensitivity analysis strategy for BN structure learning to quantify the edge importance in terms of metabolic flux prediction uncertainty reduction and its potential to effectively guide OED.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle↗
DOE OSTI2024

Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa : implications for future breeding and research studies

Abstract Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, “alongside an understanding of the genetic diversity” and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified 13 distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported and may not be universal across all organ types. From a global analysis, SG3 “was only significant higher expressed” in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

Agriculture↗
DOE OSTI2020

Generating synthetic cosmological data with GalSampler

As part of the effort to meet the needs of the Large Synoptic Survey Telescope Dark Energy Science Collaboration (LSST DESC) for accurate, realistically complex mock galaxy catalogues, in this work we have developed galsampler, an open-source python package that assists in generating large volumes of synthetic cosmological data. The key idea behind galsampler is to recast hydrodynamical simulations and semi-analytic models as physically motivated galaxy libraries. galsampler populates a new, larger volume halo catalogue with galaxies drawn from the baseline library; by using weighted sampling guided by empirical modelling techniques, galsampler inherits statistical accuracy from the empirical model and physically motivated complexity from the baseline library. We have recently used galsampler to produce the cosmoDC 2 extragalactic catalogue made for the LSST DESC Data Challenge 2 . Using cosmoDC 2 as a guiding example, we outline how galsampler can continue to support ongoing and near-future galaxy surveys such as the Dark Energy Survey, the Dark Energy Spectroscopic Instrument, WFIRST, and Euclid.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

The evolution of the Milky Way’s thin disc radial metallicity gradient with K2 asteroseismic ages

ABSTRACT The radial metallicity distribution of the Milky Way’s disc is an important observational constraint for models of the formation and evolution of our Galaxy. It informs our understanding of the chemical enrichment of the Galactic disc and the dynamical processes therein, particularly radial migration. We investigate how the metallicity changes with guiding radius in the thin disc using a sample of red giant stars with robust astrometric, spectroscopic, and asteroseismic parameters. Our sample contains 668 stars with guiding radii 4 < Rg < 11 kpc and asteroseismic ages covering the whole history of the thin disc with precision ${\approx} 25 {{\, \rm per\ cent}}$. We use MCMC analysis to measure the gradient and its intrinsic spread in bins of age and construct a hierarchical Bayesian model to investigate the evolution of these parameters independently of the bins. We find a smooth evolution of the gradient from ≈−0.07 dex kpc−1 in the youngest stars to ≈−0.04 dex kpc−1 in stars older than 10 Gyr, with no break at intermediate ages. Our results are consistent with those based on asteroseismic ages from CoRoT, with that found in Cepheid variables for stars younger than 1 Gyr, and with open clusters for stars younger than 6 Gyr. For older stars we find a significantly lower metallicity in our sample than in the clusters, suggesting a survival bias favouring more metal-rich clusters. We also find that the chemical evolution model of Chiappini '09 is too metal poor in the early stages of disc formation. Our results provide strong new constraints for the growth and enrichment of the thin disc and radial migration, which will facilitate new tests of model conditions and physics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Purple is the new green: biopigments and spectra of Earth-like purple worlds

ABSTRACT With more than 5500 detected exoplanets, the search for life is entering a new era. Using life on Earth as our guide, we look beyond green landscapes to expand our ability to detect signs of surface life on other worlds. While oxygenic photosynthesis gives rise to modern green landscapes, bacteriochlorophyll-based anoxygenic phototrophs can also colour their habitats and could dominate a much wider range of environments on Earth-like exoplanets. Here, we characterize the reflectance spectra of a collection of purple sulfur and purple non-sulfur bacteria from a variety of anoxic and oxic environments. We present models for Earth-like planets where purple bacteria dominate the surface and show the impact of their signatures on the reflectance spectra of terrestrial exoplanets. Our research provides a new resource to guide the detection of purple bacteria and improves our chances of detecting life on exoplanets with upcoming telescopes. Our biological pigment data base for purple bacteria and the high-resolution spectra of Earth-like planets, including ocean worlds, snowball planets, frozen worlds, and Earth analogues, are available online, providing a tool for modellers and observers to train retrieval algorithms, optimize search strategies, and inform models of Earth-like planets, where purple is the new green.

Coelho, Lígia Fonseca (ORCID:0000000150081249)↗
DOE OSTI2025

The role of electric dominance for particle injection in relativistic reconnection

ABSTRACT Magnetic reconnection in relativistic plasmas – where the magnetization $\sigma \gg 1$ – is regarded as an efficient particle accelerator, capable of explaining the most dramatic astrophysical flares. We employ two-dimensional (2D) particle-in-cell simulations of relativistic pair-plasma reconnection with vanishing guide field and outflow boundaries to quantify the impact of the energy gain occurring in regions of electric dominance ($E\gt B$) for the early stages of particle acceleration (i.e. the ‘injection’ stage). Given an injection threshold energy $\epsilon ^\ast =\sigma /4$ for the particles that eventually attain energy $\epsilon _{\rm T}$ by time T, we calculate the mean fractional contribution $\zeta (\epsilon ^\ast ,\epsilon _{\rm T})$ by $E\gt B$ fields to particle energization at the time when the threshold $\epsilon ^\ast$ is reached. We find that $\zeta$ monotonically increases with $\sigma$ and $\epsilon _{\rm T}$; for $\sigma \gtrsim 50$ and $\epsilon _{\rm T}/\sigma \gtrsim 8$, we find that $\gtrsim 80~{{\ \rm per\ cent}}$ of the energy gain obtained before reaching $\epsilon ^\ast =\sigma /4$ occurs in $E\gt B$ regions. We find that $\zeta$ is independent of simulation box size $L_x$, as long as $\epsilon _{\rm T}$ is normalized to the maximum particle energy, which scales as $\epsilon _{\rm max}\propto L_{\rm x}^{1/2}$ in 2D. The distribution of energy gains $\epsilon _{\chi }$ acquired in $E\gt B$ regions can be modelled as $\mathrm{ d}N/\mathrm{ d}\epsilon _{\chi }\propto \epsilon _{\chi }^{-0.35}\exp [-(\epsilon _{\chi }/0.06\, \sigma)^{0.5}]$. Our results help assess the role of electric dominance in relativistic reconnection with vanishing guide fields, which is realized in the magnetospheres of black holes and neutron stars.

Gupta, Sanya (ORCID:0000000151944384)↗
DOE OSTI2022

Improved genome editing by an engineered CRISPR-Cas12a

CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis - and trans -DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2–18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ADAR activation by inducing a syn conformation at guanosine adjacent to an editing site

Abstract ADARs (adenosine deaminases acting on RNA) can be directed to sites in the transcriptome by complementary guide strands allowing for the correction of disease-causing mutations at the RNA level. However, ADARs show bias against editing adenosines with a guanosine 5′ nearest neighbor (5′-GA sites), limiting the scope of this approach. Earlier studies suggested this effect arises from a clash in the RNA minor groove involving the 2-amino group of the guanosine adjacent to an editing site. Here we show that nucleosides capable of pairing with guanosine in a syn conformation enhance editing for 5′-GA sites. We describe the crystal structure of a fragment of human ADAR2 bound to RNA bearing a G:G pair adjacent to an editing site. The two guanosines form a Gsyn:Ganti pair solving the steric problem by flipping the 2-amino group of the guanosine adjacent to the editing site into the major groove. Also, duplexes with 2′-deoxyadenosine and 3-deaza-2′-deoxyadenosine displayed increased editing efficiency, suggesting the formation of a Gsyn:AH+anti pair. This was supported by X-ray crystallography of an ADAR complex with RNA bearing a G:3-deaza dA pair. This study shows how non-Watson–Crick pairing in duplex RNA can facilitate ADAR editing enabling the design of next generation guide strands for therapeutic RNA editing.

Doherty, Erin E.↗
DOE OSTI2023

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Evaluating the limitations of Bayesian metabolic control analysis

AbstractBayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements.Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

Shin, Janis (ORCID:0000000216572455)↗
DOE OSTI2026

Eliminating beam-induced depolarizing effects in the hydrogen jet target for high-precision proton beam polarimetry at the electron-ion collider

We analyze beam-induced depolarizing effects in the hydrogen jet target (HJET) at the relativistic heavy ion collider (RHIC), which has been used for absolute hadron beam polarimetry and shall be employed at the electron-ion collider (EIC). The EIC’s higher bunch repetition frequencies and shorter bunch durations shift beam harmonics to frequencies that can resonantly drive hyperfine transitions in hydrogen, threatening to depolarize the target atoms. Using frequency-domain analysis of beam harmonics and hyperfine transition frequencies, we establish a photon emission threshold above which beam-induced fields are too weak to cause significant depolarization. For EIC injection (23.5 GeV) and flattop (275 GeV), beam-induced depolarization through the bunch structure renders operation at the current RHIC magnetic guide field at the target (𝐵 0 =120⁢ mT) untenable. Increasing the magnetic guide field at the target to 𝐵 0 ≈ 400⁢ mT moves all hyperfine transition frequencies to at least 3 times the cutoff frequency, ensuring reliable absolute beam polarimetry with the required 1% precision at the EIC.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Lower-Hybrid Drift Waves Driving Electron Nongyrotropic Heating and Vortical Flows in a Magnetic Reconnection Layer

Here, we report measurements of lower-hybrid drift waves driving electron heating and vortical flows in an electron-scale reconnection layer under a guide field. Electrons accelerated by the electrostatic potential of the waves exhibit perpendicular and nongyrotropic heating. The vortical flows generate magnetic field perturbations comparable to the guide field magnitude. The measurements reveal a new regime of electron-wave interaction and how this interaction modifies the electron dynamics in the reconnection layer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Electron Acceleration during Macroscale Magnetic Reconnection

Here, the first self-consistent simulations of electron acceleration during magnetic reconnection in a macroscale system are presented. Consistent with solar flare observations, the spectra of energetic electrons take the form of power laws that extend more than two decades in energy. The drive mechanism for these nonthermal electrons is Fermi reflection in growing and merging magnetic flux ropes. A strong guide field suppresses the production of nonthermal electrons by weakening the Fermi drive mechanism. For a weak guide field the total energy content of nonthermal electrons dominates that of the hot thermal electrons even though their number density remains small. Our results are benchmarked with the hard x-ray, radio, and extreme ultraviolet observations of the X8.2-class solar flare on September 10, 2017.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Comment on “Nonideal Fields Solve the Injection Problem in Relativistic Reconnection”

Sironi (hereafter S22) reported the correlation between high-energy particles and their crossings of regions with electric field larger than magnetic field (E > B regions) in kinetic simulations of relativistic magnetic reconnection. They claim that E > B regions (for vanishing guide fields) accelerate particles to the injection energy γ inj ~ σ (magnetization). S22 shows that if test particles are reset to low energies in E > B regions, injection is suppressed. Here, we reexamine these claims using a simulation resembling the reference case in S22 with no guide field. We show that E > B regions contribute very little to injection (~ 10% γ inj ) as they only host particles for a short duration. The energization before any E > B crossings has a comparable contribution, indicating E > B regions are not unique for pre-acceleration. A new test-particle simulation that zeroes out E during E > B does not strongly influence injection. We suggest that the procedure to exclude E > B acceleration in S22 partly removes acceleration outside E > B, leading to a false conclusion.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Multi-GeV Electron Bunches from an All-Optical Laser Wakefield Accelerator

We present the first demonstration of multi-GeV laser wakefield acceleration in a fully optically formed plasma waveguide, with an acceleration gradient as high as 25 GeV/m . The guide was formed via self-waveguiding of < 15 J, 45 fs (< ~ 300 TW) pulses over 20 cm in a low-density hydrogen gas jet, with accelerated electron bunches driven up to 5 GeV in quasimonoenergetic peaks of relative energy width as narrow as ~ 15 % , with divergence down to ~ 1mrad and charge up to tens of picocoulombs. Energy gain is inversely correlated with on-axis waveguide density in the range Ne0 = (1.3 – 3.2) x 10 17 cm –3 . We find that shot-to-shot stability of bunch spectra and charge are strongly dependent on the pointing of the injected laser pulse and gas jet uniformity. We also observe evidence of pump depletion-induced dephasing, a consequence of the long optical guiding distance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗