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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Global relationships in tree functional traits

Due to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. Despite a wealth of studies exploring trait relationships across the entire plant kingdom, the dominant traits underpinning these unique aspects of tree form and function remain unclear. Here, by considering 18 functional traits, encompassing leaf, seed, bark, wood, crown, and root characteristics, we quantify the multidimensional relationships in tree trait expression. We find that nearly half of trait variation is captured by two axes: one reflecting leaf economics, the other reflecting tree size and competition for light. Yet these orthogonal axes reveal strong environmental convergence, exhibiting correlated responses to temperature, moisture, and elevation. By subsequently exploring multidimensional trait relationships, we show that the full dimensionality of trait space is captured by eight distinct clusters, each reflecting a unique aspect of tree form and function. Collectively, this work identifies a core set of traits needed to quantify global patterns in functional biodiversity, and it contributes to our fundamental understanding of the functioning of forests worldwide.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Selective posttranslational inhibition of Ca V β 1 -associated voltage-dependent calcium channels with a functionalized nanobody

Ca 2+ influx through high-voltage-activated calcium channels (HVACCs) controls diverse cellular functions. A critical feature enabling a singular signal, Ca 2+ influx, to mediate disparate functions is diversity of HVACC pore-forming α1 and auxiliary Ca V β 1 –Ca V β 4 subunits. Selective Ca V α 1 blockers have enabled deciphering their unique physiological roles. By contrast, the capacity to post-translationally inhibit HVACCs based on Ca V β isoform is non-existent. Conventional gene knockout/shRNA approaches do not adequately address this deficit owing to subunit reshuffling and partially overlapping functions of Ca V β isoforms. Here, we identify a nanobody (nb.E8) that selectively binds Ca V β 1 SH3 domain and inhibits Ca V β 1 -associated HVACCs by reducing channel surface density, decreasing open probability, and speeding inactivation. Functionalizing nb.E8 with Nedd4L HECT domain yielded Chisel-1 which eliminated current through Ca V β 1 -reconstituted Ca V 1/Ca V 2 and native Ca V 1.1 channels in skeletal muscle, strongly suppressed depolarization-evoked Ca 2+ influx and excitation-transcription coupling in hippocampal neurons, but was inert against Ca V β 2 -associated Ca V 1.2 in cardiomyocytes. The results introduce an original method for probing distinctive functions of ion channel auxiliary subunit isoforms, reveal additional dimensions of Ca V β 1 signaling in neurons, and describe a genetically-encoded HVACC inhibitor with unique properties.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes

Plasmids play significant roles in microbial adaptation to ecosystems, yet their dynamics remain poorly understood due to identification challenges. We present the Global Soil Plasmidome Resource (GSPR), a comprehensive dataset of 98,728 plasmid sequences amassed from 6860 terrestrial microbial communities and isolates. We explore this resource through various computational approaches, including phylogenetic diversity analysis, host prediction, and extensive functional annotation, to understand the contribution of plasmids to the genetic and functional diversity in soil, correlating these findings with sample type, as well as the soil habitat they were retrieved from. Our analysis reveals insights into plasmid-encoded functions such as effector modules, quorum sensing, and stress resistance, which may contribute to their persistence and microbial adaptation in soil. Furthermore, CRISPR analysis suggests a prevalent role of these elements related to intra-plasmid competition. By contrasting plasmids from cultivated and uncultivated organisms, we identify important functions that expand existing knowledge of plasmid roles in these habitats. This study represents a notable step forward in elucidating plasmid diversity and function within soil microbiomes and establishes a foundational framework for exploring their roles in natural environments.

Fiamenghi, Mateus B↗
DOE OSTI2023

Non-adiabatic approximations in time-dependent density functional theory: progress and prospects

Time-dependent density functional theory continues to draw a large number of users in a wide range of fields exploring myriad applications involving electronic spectra and dynamics. Although in principle exact, the predictivity of the calculations is limited by the available approximations for the exchange-correlation functional. In particular, it is known that the exact exchange-correlation functional has memory-dependence, but in practise adiabatic approximations are used which ignore this. Here we review the development of non-adiabatic functional approximations, their impact on calculations, and challenges in developing practical and accurate memory-dependent functionals for general purposes.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Multiple elements of soil biodiversity drive ecosystem functions across biomes

The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Furthermore, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d

Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A functional microbiome catalogue crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Copper-dependent halogenase catalyses unactivated C−H bond functionalization

Carbon–hydrogen (C–H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp 3 )−H bond. In recent years, metalloenzymes have been found to perform C(sp 3 )−H bond functionalization. Despite substantial progresses in the past two decades, enzymatic halogenation and pseudohalogenation of unactivated C(sp 3 )−H—providing a functional handle for further modification—have been achieved with only non-haem iron/α-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes. Here, in this work, we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp 3 )−H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp 3 )−H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs—one interchain and two intrachain—of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp 3 )−H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.

biocatalysis↗
DOE OSTI2022

Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles place uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO 2 -concentrating mechanism and ciliogenesis. We illustrate the value of this resource by validating phenotypes and gene functions, including three new components of an actin cytoskeleton defense pathway. The data also inform phenotype discovery in land plants; mutants in Arabidopsis thaliana genes exhibit phenotypes similar to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dark matter halo mass functions and density profiles from mass and energy cascade

Abstract Halo abundance and structure play a central role for modeling structure formation and evolution. Without relying on a spherical or ellipsoidal collapse model, we analytically derive the halo mass function and cuspy halo density (inner slope of −4/3) based on the mass and energy cascade theory in dark matter flow. The hierarchical halo structure formation leads to halo or particle random walk with a position-dependent waiting time $$\tau _g$$ τ g . First, the inverse mass cascade from small to large scales leads to the halo random walk in mass space with $$\tau _g\propto m_h^{-\lambda }$$ τ g ∝ m h - λ , where $$m_h$$ m h is the halo mass and $$\lambda$$ λ is a halo geometry parameter with predicted value of 2/3. The corresponding Fokker-Planck solution for halo random walk in mass space gives rise to the halo mass function with a power-law behavior on small scale and exponential decay on large scale. This can be further improved by considering two different $$\lambda$$ λ for haloes below and above a critical mass scale $$m_h^*$$ m h ∗ , i.e. a double- $$\lambda$$ λ halo mass function. Second, a double- $$\gamma$$ γ density profile can be derived based on the particle random walk in 3D space with a position-dependent waiting time $$\tau _g \propto \Phi (r)^{-1} \propto r^{-\gamma }$$ τ g ∝ Φ ( r ) - 1 ∝ r - γ , where $$\Phi$$ Φ is the gravitational potential and r is the particle distance to halo center. Theory predicts $$\gamma =2/3$$ γ = 2 / 3 that leads to a cuspy density profile with an inner slope of −4/3, consistent with the predicted scaling laws from energy cascade. The Press-Schechter mass function and Einasto density profile are just special cases of proposed models. The small scale permanence can be identified due to the scale-independent rate of mass and energy cascade, where density profiles of different halo masses and redshifts converge to the $$-4/3$$ - 4 / 3 scaling law ( $$\rho _h \propto r^{-4/3}$$ ρ h ∝ r - 4 / 3 ) on small scales. Theory predicts the halo number density scales with halo mass as $$\propto m_h^{-1.9}$$ ∝ m h - 1.9 , while the halo mass density scales as $$\propto m_h^{4/9}$$ ∝ m h 4 / 9 . Results were compared against the Illustris simulations. This new perspective provides a theory for nearly universal halo mass functions and density profiles.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Amine-functionalized porous organic polymers for carbon dioxide capture

Recent developments in CO 2 capture using porous organic polymers (POPs) have received accrescent attention due to their sorbent properties such as high CO 2 uptake capacity and selectivity, tunable chemical structure and permanent porosity. POPs are constructed using two and/or three-dimensional organic monomers (building blocks) linked to each other through covalent bonding, creating high porosity. The pore structure in POPs is exceptionally stable, which leads to their cyclable CO 2 adsorption performance. However, POPs generally suffer from low CO 2 uptake and selectivity due to their interaction with CO 2 in physisorption limits (20–40 kJ mol -1 ). Similar to that in other physisorbents, the CO 2 uptake capacity of POPs further decreases under humid conditions. Pursuant to these limitations, amine functionalization in POPs has resulted in enhanced CO 2 uptake performance with improved CO 2 selectivity over non-polar gases such as N 2 . More importantly, several types of amine-functionalized POPs showed that the CO 2 uptake could remain intact under humid conditions such as in post-combustion flue gas. This review article covers recent developments in amine-functionalized porous organic polymers. Three main categories of amine functionalization, such as direct amine synthesis, amine impregnation and amine grafting, were investigated in detail by considering the effect of amines on the sorbent properties and CO 2 capture performance of POPs. The recent findings in amine-functionalized POPs were investigated including porous polymeric networks (PPNs), covalent organic frameworks (COFs), amine linked POPs, hyper-crosslinked polymers (HCPs), conjugated microporous polymers (CMPs), benzimidazole linked polymers (BILPs), porous aromatic frameworks (PAFs) and polymers of intrinsic microporosity (PIMs).

36 MATERIALS SCIENCE↗
DOE OSTI2024

Delocalization error poisons the density-functional many-body expansion

The many-body expansion is a fragment-based approach to large-scale quantum chemistry that partitions a single monolithic calculation into manageable subsystems. This technique is increasingly being used as a basis for fitting classical force fields to electronic structure data, especially for water and aqueous ions, and for machine learning. Here, we show that the many-body expansion based on semilocal density functional theory affords wild oscillations and runaway error accumulation for ion–water interactions, typified by F − (H 2 O) N with N ≳ 15. We attribute these oscillations to self-interaction error in the density-functional approximation. The effect is minor or negligible in small water clusters, explaining why it has not been noticed previously, but grows to catastrophic proportion in clusters that are only moderately larger. This behavior can be counteracted with hybrid functionals but only if the fraction of exact exchange is ≳50%, whereas modern meta-generalized gradient approximations including ωB97X-V, SCAN, and SCAN0 are insufficient to eliminate divergent behavior. Other mitigation strategies including counterpoise correction, density correction (i.e., exchange–correlation functionals evaluated atop Hartree–Fock densities), and dielectric continuum boundary conditions do little to curtail the problematic oscillations. In contrast, energy-based screening to cull unimportant subsystems can successfully forestall divergent behavior. These results suggest that extreme caution is warranted when the many-body expansion is combined with density functional theory.

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

Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments

Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation and the exploration of the potential application of DNA strands in nanoelectronics. In this work, by employing our recently developed Green’s function coupled-cluster library on supercomputing facilities, we have studied the spectral functions of several guanine–cytosine (G–C) base pair structures ([G–C]n, n = 1–3) for the first time in a relatively broad near-valence regime ([−25.0, −5.0] eV) in the coupled-cluster with singles and doubles level. Our focus is to give a preliminary many-body coupled-cluster understanding and guideline of the vertical ionization energy (VIE), spectral profile, and ionization feature changes of these systems as the system size expands in this near-valence regime. The results show that, as the system size expands, even though the lowest VIEs keep decreasing, the changes of spectral function profile and the relative peak positions get unexpectedly smaller. Further analysis of the ionized states associated with the most intensive peak in the spectral functions reveals non-negligible |2h, 1p⟩’s in the ionized wave functions of the considered G–C base pair systems. The leading |2h, 1p⟩’s associated with the main ionizations from the cytosine part of the G–C base pairs feature a transition from the intra-base-pair cytosine π → π* excitation to the inter-base-pair electron excitation as the size of G–C base pairs expands, which also indicates the minimum quantum region in the many-body calculations of DNA systems.

Peng, Bo (ORCID:0000000242267294)↗
DOE OSTI2020

Guided search for desired functional responses via Bayesian optimization of generative model: Hysteresis loop shape engineering in ferroelectrics

Advances in theoretical modeling across multiple disciplines have yielded generative models capable of high veracity in predicting macroscopic functional responses of materials emerging as a result of complex non-local interactions. Correspondingly, of interest is the inverse problem of finding the model parameter that will yield desired macroscopic responses, such as stress–strain curves, ferroelectric hysteresis loops, etc. Here, we suggest and implement Gaussian process based methods that allow to effectively sample the degenerate parameter space of a complex non-local model to output regions of parameter space which yield desired functionalities. In this work, we discuss the specific adaptation of the acquisition function and sampling function to make the process efficient and balance the efficient exploration of parameter space for multiple possible minima and exploitation to densely sample the regions of interest where target behaviors are optimized. Additionally, this approach is illustrated via the hysteresis loop engineering in ferroelectric materials but can be adapted to other functionalities and generative models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Experimental observations of exploding bridgewire detonator function

Exploding bridgewire detonators are an industry standard technology used for over 75 years and valued for their precise timing and safety characteristics. Despite widespread use, their functional mechanism remains controversial with both shock and non-shock mechanisms attributed. In this work, we re-examine bridgewire detonator function with a suite of modern diagnostics and compare these observations with the existing literature. Traditional detonator observations consisted of voltage applied to the bridgewire and time dependent current, integral response measurements such as case motion and more recently Schlieren imaging of the detonator surface. In this work, we add visible light emission, X-ray transmission, proton radiography, and temperature measurements during detonator function in addition to voltage, current, and function times. The addition of in-situ observations of light emission, temperature, and density gives us new insight into the mechanisms of explosive bridgewire detonator function. We see a distinct separation in time, location, symmetry, and velocity of bridgewire output and detonation onset. During the time between bridgewire burst and the initiation of detonation, we observe a temperature ramp in the input pellet. In this paper, we present the suite of measurements and comparisons with the literature on integral response measurements.

42 ENGINEERING↗
DOE OSTI2021

Statistical analysis of non-Maxwellian electron distribution functions measured with angularly resolved Thomson scattering

Angularly resolved Thomson scattering is a novel extension of Thomson scattering, enabling the measurement of the electron velocity distribution function over many orders of magnitude. Here, details of the theoretical basis of the technique and the instrument designed for this measurement are described. Angularly resolved Thomson-scattering data from several experiments are shown with descriptions of the corresponding distribution functions. A reduced model describing the distribution function is given and used to perform a Monte Carlo analysis of the uncertainty in the measurements. The electron density and temperature were determined to a precision of 12% and 21%, respectively, on average, while all other parameters defining the distribution function were generally determined to better than 20%. It was found that these uncertainties were primarily due to limited signal to noise and instrumental effects. Furthermore, measurements with this level of precision were sufficient to distinguish between Maxwellian and non-Maxwellian distribution functions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Constructing tensor network influence functionals for general quantum dynamics

Here, we describe an iterative formalism to compute influence functionals that describe the general quantum dynamics of a subsystem beyond the assumption of linear coupling to a quadratic bath. We use a space-time tensor network representation of the influence functional and investigate its approximability in terms of its bond dimension and time-like entanglement in the tensor network description. We study two numerical models, the spin-boson model and a model of interacting hard-core bosons in a 1D harmonic trap. We find that the influence functional and the intermediates involved in its construction can be efficiently approximated by low bond dimension tensor networks in certain dynamical regimes, which allows the quantum dynamics to be accurately computed for longer times than with direct time evolution methods. However, as one iteratively integrates out the bath, the correlations in the influence functional can first increase before decreasing, indicating that the final compressibility of the influence functional is achieved via non-trivial cancellation.

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

Bootstrap estimation of the effect of instrument response function uncertainty on the reconstruction of fusion neutron sources

Neutron imagers are important diagnostics for the inertial confinement fusion implosions at the National Ignition Facility. They provide two- and three-dimensional reconstructions of the neutron source shape that are key indicators of the overall performance. To interpret the shape results properly, it is critical to estimate the uncertainty in those reconstructions. There are two main sources of uncertainties: limited neutron statistics, leading to random errors in the reconstructed images, and incomplete knowledge of the instrument response function (the pinhole-dependent point spread function). While the statistical errors dominate the uncertainty for lower yield deuterium-tritium (DT) shots, errors due to the instrument response function dominate the uncertainty for DT yields on the order of 10 16 neutrons or higher. In this work, a bootstrapping method estimates the uncertainty in a reconstructed image due to the incomplete knowledge of the instrument response function. The main reconstruction is created from the fixed collection of pinhole images that are best aligned with the neutron source. Additional reconstructions are then built using subsets of that collection of images. Variations in the shapes of these additional reconstructions originate solely from uncertainties in the instrument response function, allowing us to use them to provide an additional systematic uncertainty estimate.

47 OTHER INSTRUMENTATION↗