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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Clustering Nuclear Magnetic Resonance: Machine learning assistive rapid two‐dimensional relaxometry mapping

Abstract Low‐field nuclear magnetic resonance (NMR) relaxometry is an attractive approach from point‐of‐care testing medical diagnosis to in situ oil‐gas exploration. One of the problems, however, is the inherently long relaxation time of the (liquid) samples, (and hence low signal‐to‐noise ratio) which causes unnecessarily long repetition time. In this work, a new class of methodology is presented for rapid and accurate object classification using NMR relaxometry with the aid of machine learning. It is demonstrated that the sensitivity and specificity of the classification is substantially improved with higher order of (pseudo)‐dimensionality (e.g., 2D‐ or multi‐dimensional). This new methodology (termed as ‘Clustering NMR’) may be extremely useful for rapid and accurate object classification (in less than a minute) using low‐field NMR.

Peng, Weng Kung↗
DOE OSTI2021

Rapid In Situ Ligand‐Exchange Process Used to Prepare 3D PbSe Nanocrystal Superlattice Infrared Photodetectors

Abstract Colloidal semiconductor nanocrystals are important building blocks for low‐cost, solution‐processed electronic devices with tunable functionalities. Considerable progress is made in improving charge transport through nanocrystal films by exchanging long insulating ligands with shorter passivating ligands. To take full advantage of this strategy, it is equally important to fabricate close‐packed structures that reduce the average interparticle spacing. Yet it remains a challenge to retain long‐range, close‐packed order after ligand exchange. Here, a novel one‐step in situ ligand‐exchange method is demonstrated that enables rapid (5 min) ligand exchange of nanocrystal films, which are more than 50 layers thick. Using this simple and efficient method, it is shown that the face‐centered cubic ordering of 500 nm thick PbSe nanocrystal films is retained after ligand exchange from oleic acid to benzoic acid. Moreover, it is demonstrated that PbSe nanocrystal photodetectors with a well‐ordered structure have superior optoelectronic properties compared to disordered films; ordered films have a 16× higher responsivity of ≈0.25 A W −1 at 1 V and a 2× faster response time. As far as it is known, this is the first report to realize a rapid one‐step ligand exchange through a thick superlattice film with retention of long‐range order.

infrared detecton↗
DOE OSTI2025

Spatial‐Uniformity–Driven Bayesian Optimization for Rapid Development of Printed Perovskite Solar Cells

Printed metal halide perovskites can enable rapid, roll-to-roll manufacturing of a broad class of optoelectronics—flexible solar cells and imagers among them—while promising cost and speed advantages over incumbent silicon. However, though current methods offer high throughput and patterning capabilities, perovskite films’ spatial heterogeneity remains a challenge for large-area devices. Here, a spatial-uniformity-driven Bayesian optimization (BO) approach is leveraged to accelerate the development of printed perovskite solar cells and improve large-area device performance. Using a BO surrogate model, a 6D design space of ink chemistry and printing physics is explored via extensive iterative experimentation (≈100) informed by an objective function capturing spatial photoluminescence (PL) variance. It is discovered that optimizing for uniformity drives rapid advances in photovoltaic performance, yielding ≈20% power conversion efficiency (PCE) for small area (0.134 cm 2 ) devices and > 16% for large area (1 cm 2 ) devices. This machine-learning approach simultaneously enables rheological comparison of ink formulations that accelerate the leveling of Saffman-Taylor artifacts and improve film uniformity. Here, this showcases uniformity-driven BO as an efficient approach for uncovering the key printing physics and mitigating spatial heterogeneity to enable device scaling beyond small cell areas.

14 SOLAR ENERGY↗
DOE OSTI2020

A Rapid Population Assessment Method for Wild Pigs Using Baited Cameras at 3 Study Sites

ABSTRACT Reliable and efficient population estimates are a critical need for effective management of invasive wild pigs ( Sus scrofa ). We evaluated the use of 10‐day camera grids for rapid population assessment (RPA) of wild pigs at 3 study sites that varied in vegetation communities and wild pig densities. Study areas included Buck Island Ranch, Florida; Tejon Ranch, California; and the Savannah River Site, South Carolina, USA, during 2016–2018. Rapid population assessments grids were composed of baited camera traps spaced approximately 500 or 750 m apart. Two RPA grids were deployed per study site and each grid was deployed twice (4–6 months apart) to assess changes in response to season or population control efforts. We assessed the ability of RPA grids to track population trends, how camera number influenced estimate precision, and how relative abundance indices related to density estimates. We detected changes in occupancy probability, detection probability, and N‐mixture estimates following removal operations and between seasons, but the ability of RPA grids to track population trends was dependent on the statistical method used and number of cameras traps. Increasing the number of cameras traps used in RPA grids increased precision, and these results can be used in determining survey design and estimate choice. We found that estimates of occupancy probability, detection probability, and N‐mixture estimates were positively correlated with spatially explicit capture–recapture density estimates. Thus, these less labor‐intensive estimates from RPA grids showed potential to index the relative abundance of wild pigs in some systems. Our evaluation of RPAs indicates that using study‐specific combinations of statistical method and number of cameras can provide a useful tool for monitoring wild pig presence, tracking population trends, and evaluating the effectiveness of management actions. © 2020 The Wildlife Society.

Schlichting, Peter E.↗
DOE OSTI2020

Studies of J/ψ production at forward rapidity in Pb–Pb collisions at $\sqrt{s_{\mathrm{NN}}}$ = 5.02 TeV

The inclusive J/ψ production in Pb–Pb collisions at the center-of-mass energy per nucleon pair $\sqrt{s_{\mathrm{NN}}}$ = 5.02 TeV, measured with the ALICE detector at the CERN LHC, is reported. The J/ψ meson is reconstructed via the dimuon decay channel at forward rapidity (2.5 < y < 4) down to zero transverse momentum. The suppression of the J/ψ yield in Pb–Pb collisions with respect to binary-scaled pp collisions is quantified by the nuclear modification factor (R AA ). The R AA at $\sqrt{s_{\mathrm{NN}}}$ = 5.02 TeV is presented and compared with previous measurements at $\sqrt{s_{\mathrm{NN}}}$= 2.76 TeV as a function of the centrality of the collision, and of the J/ψ transverse momentum and rapidity. The inclusive J/ψ R AA shows a suppression increasing toward higher transverse momentum, with a steeper dependence for central collisions. The modification of the J/ψ average transverse momentum and average squared transverse momentum is also studied. Comparisons with the results of models based on a transport equation and on statistical hadronization are carried out.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Completely dark matter from rapid-turn multifield inflation

We study cosmological gravitational particle production as applied to “rapid-turn” models of inflation involving two scalar fields. We are interested in the production of massive spin-0 particles that only interact gravitationally and provide a candidate for the dark matter. Specifically, we study two models of rapid-turn multifield inflation, motivated in part by the de Sitter swampland conjecture, that are distinguished by the curvature of field space and the presence or absence of field space ‘angular momentum’ conservation. We find that one of these models leads to insufficient particle production and cannot explain the observed dark matter relic abundance. The second model is able to explain the origin of spin-0 dark matter via gravitational production, and we identify the relevant region of parameter space that is consistent with measurements of the dark-matter relic abundance, the dark-matter-photon isocurvature perturbations, and the spectrum of curvature perturbations that is probed by cosmological observations. Our work demonstrates the compatibility of the de Sitter swampland conjecture with completely dark matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Study of dijet events with large rapidity separation in proton-proton collisions at $\sqrt{s}$ = 2.76 TeV

The cross sections for inclusive and Mueller-Navelet dijet production are measured as a function of the rapidity separation between the jets in proton-proton collisions at $\sqrt{s}$ = 2.76 TeV for jets with transverse momentum p T > 35 GeV and rapidity |y| < 4.7. Various dijet production cross section ratios are also measured. A veto on additional jets with p T > 20 GeV is introduced to improve the sensitivity to the effects of the Balitsky-Fadin-Kuraev-Lipatov (BFKL) evolution. The measurement is compared with the predictions of various Monte Carlo models based on leading-order and next-to-leading-order calculations including the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi leading-logarithm (LL) parton shower as well as the LL BFKL resummation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Rapidity-only TMD factorization at one loop

Typically, a production of a particle with a small transverse momentum in hadron-hadron collisions is described by CSS-based TMD factorization at moderate Bjorken x B ~ 1 and by k T -factorization at small x B . A uniform description valid for all x B is provided by rapidity-only TMD factorization developed in a series of recent papers at the tree level. In this paper the rapidity-only TMD factorization for particle production by gluon fusion is extended to the one-loop level.

deep inelastic scattering↗
DOE OSTI2022

Forward rapidity $J/ψ$ production as a function of charged-particle multiplicity in pp collisions at $\sqrt{s}$ = 5.02 and 13 TeV

The production of J/ψ is measured as a function of charged-particle multiplicity at forward rapidity in proton-proton (pp) collisions at center-of-mass energies $\sqrt{s}$ = 5.02 and 13 TeV. The J/ψ mesons are reconstructed via their decay into dimuons in the rapidity interval (2.5 < y < 4.0), whereas the charged-particle multiplicity density (dN ch /dη) is measured at midrapidity (|η| <; 1). The production rate as a function of multiplicity is reported as the ratio of the yield in a given multiplicity interval to the multiplicity-integrated one. This observable shows a linear increase with charged-particle multiplicity normalized to the corresponding average value for inelastic events (dN ch /dη/$\langle$dN ch /dη$\rangle$), at both the colliding energies. Measurements are compared with available ALICE results at midrapidity and theoretical model calculations. First measurement of the mean transverse momentum ($\langle$p T $\rangle$) of J/ψ in pp collisions exhibits an increasing trend as a function of dN ch /dη/$\langle$dN ch /dη$\rangle$ showing a saturation towards high charged-particle multiplicities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Multiplicity-dependent inclusive J/ ψ production at forward rapidity in pp collisions at $\sqrt{s}$ = 13 TeV

This paper presents a study of the inclusive forward J/ψ yield as a function of forward charged-particle multiplicity in pp collisions at $\sqrt{s}$ = 13 TeV using data collected by the ALICE experiment at the CERN LHC. The results are presented in terms of relative J/ψ yields and relative charged-particle multiplicities with respect to these quantities obtained in inelastic collisions having at least one charged particle in the pseudorapidity range |η| < 1. The J/ψ mesons are reconstructed via their decay into μ + μ − pairs in the forward rapidity region (2.5 < y < 4). The relative multiplicity is estimated in the forward pseudorapidity range which overlaps with the J/ψ rapidity region. The results show a steeper-than-linear increase of the J/ψ yields versus the multiplicity. They are compared with previous measurements and theoretical model calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

A rapid heating and high magnetic field thermal analysis technique

Abstract A new thermal analysis technique is described that allows measurements to be performed on bulk samples at extreme heating and cooling rates and in high magnetic fields. High heating rates, up to 1000 °C min −1 , are achieved through electromagnetic induction heating of a custom-built apparatus fitted with commercial thermal analysis heads and sensor. Rapid cooling rates, up to 100 °C min −1 , are enabled by gas quenching and the small thermal mass of the induction furnace. The custom apparatus is designed to fit inside a superconducting magnet capable of fields up to 9 Tesla. This study demonstrates that the instrument is capable of collecting accurate thermal analysis data in high magnetic fields and rapidly acquiring data for dynamic processes. While the full potential of the technique is still unrealized, currently, it can provide insight into phenomena at time scales relevant to heat treatment in many industrial processes and into little understood effects of high magnetic field processing.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Rapidly Changing Range Limits in a Warming World: Critical Data Limitations and Knowledge Gaps for Advancing Understanding of Mangrove Range Dynamics in the Southeastern USA

Climate change is altering species’ range limits and transforming ecosystems. For example, warming temperatures are leading to the range expansion of tropical, cold-sensitive species at the expense of their cold-tolerant counterparts. In some temperate and subtropical coastal wetlands, warming winters are enabling mangrove forest encroachment into salt marsh, which is a major regime shift that has significant ecological and societal ramifications. Here, we synthesized existing data and expert knowledge to assess the distribution of mangroves near rapidly changing range limits in the southeastern USA. We used expert elicitation to identify data limitations and highlight knowledge gaps for advancing understanding of past, current, and future range dynamics. Mangroves near poleward range limits are often shorter, wider, and more shrublike compared to their tropical counterparts that grow as tall forests in freeze-free, resource-rich environments. The northern range limits of mangroves in the southeastern USA are particularly dynamic and climate sensitive due to abundance of suitable coastal wetland habitat and the exposure of mangroves to winter temperature extremes that are much colder than comparable range limits on other continents. Thus, there is need for methodological refinements and improved spatiotemporal data regarding changes in mangrove structure and abundance near northern range limits in the southeastern USA. Advancing understanding of rapidly changing range limits is critical for foundation plant species such as mangroves, as it provides a basis for anticipating and preparing for the cascading effects of climate-induced species redistribution on ecosystems and the human communities that depend on their ecosystem services.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Pseudo-rapidity distributions of charged particles in asymmetric collisions using Tsallis thermodynamics

Abstract The pseudo-rapidity distributions of the charged particles produced in the asymmetric collision systems p+Al, p+Au and$$^3$$ 3 He+Au at$$\sqrt{s_\text {NN}} = 200$$ s NN = 200 GeV are evaluated in the framework of a fireball model with Tsallis thermodynamics. The fireball model assumes that the experimentally measured particles are produced by fireballs following the Tsallis distribution and it can effectively describe the experimental data. Our results as well as previous results for d+Au collisions at$$\sqrt{s_\text {NN}} = 200$$ s NN = 200 GeV and p+Pb collisions at$$\sqrt{s_\text {NN}} = 5.02$$ s NN = 5.02 TeV validate that the fireball model based on Tsallis thermodynamics can provide a universal framework for pseudo-rapidity distribution of the charged particles produced in asymmetric collision systems. We predict the centrality dependence of the total charged particle multiplicity in the p+Al, p+Au and$$^3$$ 3 He+Au collisions. Additionally, the dependences of the fireball model parameters ($$y_{0a}$$ y 0 a ,$$y_{0A}$$ y 0 A ,$$\sigma _{a}$$ σ a and$$\sigma _{A}$$ σ A ) on the centrality and system size are studied.

Nuclear Science & Technology↗
DOE OSTI2025

New capabilities for rapid depletion analysis of pebble-bed reactors in SCALE

The SCALE Leap-In for Cores at Equilibrium (SLICE) method leverages capabilities available in the SCALE modeling and simulation suite to facilitate rapid estimation of equilibrium core inventories for flowing-pebble reactor systems in support of a variety of fuel cycle applications. New capabilities that compliment the SLICE method have been developed for the ORIGAMI interface to ORIGEN in SCALE to facilitate rapid depletion calculations for flowing-pebble systems. New features include a more generalized and flexible means of specifying interpolation dimensions, the ability to evaluate pebbles moving through user-defined “axial zones” in each of the pebble’s multiple passes through the core, and the treatment of differential velocities across radial channels (representing both pebble-to-pebble and wall-to-pebble friction effects). ORIGAMI thus provides an efficient user interface to define a pebble’s path and irradiation histories of its multiple passes through the core to calculate the pebble’s time-dependent inventories, which can be useful in various applications domains such as safeguards, criticality safety, and disposal analyses. The consistency of new ORIGAMI approach was verified against the solution obtained using the SLICE method with ORIGEN-ARP, showing excellent agreement.

Skutnik, Steven E. [Oak Ridge National Laboratory ↗
DOE OSTI2023

Rapid increase in tropospheric ozone over Southeast Asia attributed to changes in precursor emission source regions and sectors

Observations indicate that tropospheric ozone (O 3 ) concentrations over Southeast Asia have been increasing rapidly since the 1990s. Here, we quantify source contributions from geographical regions and emission sectors of the two distinct types of O 3 precursors, i.e., nitrogen oxides (NO x ) and volatile organic compounds (VOCs), to the increase in tropospheric O 3 in Southeast Asia during 1990–2019 using an O 3 source tagging technique implemented in a global chemistry-climate model. In this work, the results show that although local anthropogenic emission of NO x in Southeast Asia only contributes 18% of the annual averaged near-surface O 3 concentration, the increase in local NO x emission dominates the increasing trend of O 3 concentration in Southeast Asia, accounting for 107% of the regional averaged trend of 1.07 ppb decade -1 . Increases in NO x emissions from East Asia and South Asia explain 29% of the increasing trend, but 9% is offset by the emission reduction in North America. Ground transportation is responsible for 79% of the rapid O 3 increase, followed by 39% contribution from international shipping. Because an increase in anthropogenic NO x emissions enhances the O 3 production efficiency by VOCs, the increase in near-surface O 3 concentrations in Southeast Asia is thereby largely contributed by methane and biogenic VOCs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Rapid and high-throughput determination of sorghum ( Sorghum bicolor ) biomass composition using near infrared spectroscopy and chemometrics

Compositional characterization of biomass is vital for the biofuel industry. Traditional wet chemistry-based methods for analyzing biomass composition are laborious, time-consuming, and require extensive use of chemical reagents as well as highly skilled personnel. In this study, near-infrared (NIR) spectroscopy was used to quickly assess the composition of above-ground vegetative biomass from 113 diverse, photoperiod-sensitive, biomass-type sorghum (Sorghum bicolor) accessions cultivated under field conditions in Central Illinois. Biomass samples were analyzed using NIR spectra collected in the spectral range of 867–2536 nm, with their chemical compositions determined following the National Renewable Energy Laboratory (NREL) protocol. Advanced spectral pre-treatment and band selection techniques were utilized to develop calibration models using partial least squares regression (PLSR). The models’ effectiveness was assessed through cross-validation and independent data tests. The predictions for moisture, ash, extractives, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin were accurate and reliable, demonstrating the capability of NIR spectroscopy to provide rapid and precise characterization of sorghum biomass. The results demonstrated that NIR spectroscopy is an efficient tool for rapidly characterizing sorghum biomass, making it a sustainable option for screening desirable feedstock for biofuel or bioproduct production.

09 BIOMASS FUELS↗
DOE OSTI2020

Dielectrophoresis assisted rapid, selective and single cell detection of antibiotic resistant bacteria with G-FETs

Time-consuming, expensive and low sensitivity diagnostic methods used for monitoring bacterial infections lead to unnecessary or delays in prescription of the right antibiotic treatment. Determining an optimal clinical treatment requires rapid detection and identification of pathogenic bacteria and their sensitivity to specific antimicrobials. However, diagnostic devices that meet all of these criteria have proven elusive thus far. Graphene field effect transistors (G-FET) are a promising solution, since they are highly sensitive to chemical/biological modification, can have fast detection times and can be placed on different substrates. Here, by integrating specific peptide probes over G-FETs, we present a proof-of-concept study for species and strain specific label-free detection of clinical strains of pathogenic bacteria with high specificity and sensitivity. We found that pyrene-conjugated peptides immobilized on G-FETs were capable of detecting pathogenic Staphylococcus aureus at the single-cell level and discriminate against other gram-positive and gram-negative bacterial pathogens. A similar device was able to discriminate between antibiotic resistant and sensitive strains of Acinetobacter baumannii , suggesting that these devices can also be used for detecting antibiotic resistive pathogens. Furthermore, a new means of enhancing attachment, electric-field assisted binding, reduced the detection limit to 104 cells/ml and the detection time to below 5 minutes. Here, the combination of single step attachment, inexpensive production, rapid, selective and sensitive detection suggest G-FETs plus pyrene-conjugated peptides are a new platform for solving major challenges faced in point of care diagnostics to fight infectious diseases and antimicrobial resistance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗