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NASA NTRS2011

Deep Diversity: Novel Approach to Overcoming the PCR Bias Encountered During Environmental Analysis of Microbial Populations for Alpha-Diversity

Alpha-diversity studies are of crucial importance to environmental microbiologists. The polymerase chain reaction (PCR) method has been paramount for studies interrogating microbial environmental samples for taxon richness. Phylogenetic studies using this technique are based on the amplification and comparison of the 16S rRNA coding regions. PCR, due disproportionate distribution of microbial species in the environment, increasingly favors the amplification of the most predominant phylotypes with every subsequent reaction cycle. The genetic and chemical complexity of environmental samples are intrinsic factors that exacerbate an inherit bias in PCR-based quantitative and qualitative studies of microbial communities. We report that treatment of a genetically complex total genomic environmental DNA extract with Propidium Monoazide (PMA), a DNA intercalating molecule capable of forming a covalent cross-linkage to organic moieties upon light exposure, disproportionally inactivates predominant phylotypes and results in the exponential amplification of previously shadowed microbial ?-diversity quantified as a 19.5% increase in OUTs reported via phylogenetic screening using PhyloChip.

phylogenetic microarray technologies↗

DOE OSTI2025

A Thorough Characterization of the Tellurocyanate Anion

Tellurocyanate, [TeCN] − , is the heaviest group 16 congener of the cyanate anion, [OCN] − . Due to the relative instability of the C─Te bond, tellurocyanate chemistry has seen only scarce attention. Here, we present the facile synthesis and thorough characterization of [K@crypt-222][TeCN]. The anion is essentially linear with interatomic distances C─N = 1.150(6)Å and C─Te = 2.051(4)Å, thus approximating a C≡N triple bond and for C─Te a bond order between 1 and 2. Fully 13 C and 15 N labeled [Te 13 C 15 N] − allowed for the extraction of chemical shifts and all possible coupling constants ( 13 C = 77.8 ppm, 15 N = 285.7 ppm, 125 Te = −566 ppm, 1 J 13C-15N = 8 Hz, 1 J 13C-125Te = 748 Hz, 2 J1 5N-125Te = 55 Hz), which were also determined independently by quantum chemical calculations. In the series [ChCN] − (Ch = O─Te), [TeCN] − shows the strongest spin-orbit coupling (SOC) induced heavy-atom effect on the light-atom shielding (SO-HALA-effect). In contrast, 15 N shifts are also well described without considering relativistic effects and/or SOC. Negative-ion photoelectron spectroscopy was used to extract the electron affinity (EA = 3.034 eV) and spin-orbit splitting (3807 cm −1 ) of [TeCN] • . These values continue the trends of falling EA and rising SOC in the series [ChCN] • .

Bonding analysis↗

DOE OSTI2021

Advances in scientific literature mining for interpreting materials characterization

Abstract Using synchrotron light sources, such as the National Synchrotron Light Source II at Brookhaven National Laboratory, scientists in fields as diverse as physics, biology, and materials science, identify the atomic structure, chemical composition, or other important properties of varied specimens. x-ray spectroscopy from light sources is particularly valuable for materials research with vast information available about reference spectra in the scientific literature. However, as the technique is applicable to many science domains, searching for information about select x-ray spectroscopy spectra is impeded by the sheer number of publications. Moreover, useful information about the context of an experiment or figures presented in papers can be buried among the details, which takes time to assess. This work presents a scientific literature mining system that supports data acquisition, information extraction, and user interaction for referencing x-ray spectra identification and spectral interpretation. The goal is to provide efficient access to useful spectral data to researchers who may spend only a few days at a synchrotron light source. With this system, users browse a classification tree for papers arranged according to x-ray spectroscopic methods, chemical elements, and x-ray absorption spectroscopy edges. Relevant figures are extracted with sentences from the paper that explain them, known as ‘figure explanatory text.’ Notably, this system focuses on semantic aspects (logical analysis) to find figure explanatory text using deep contextualized word embeddings techniques and contains an interface to obtain labeled data from domain experts that is used to evaluate and improve the model.

Park, Gilchan (ORCID:0000000201536646)↗

DOE OSTI2020

Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold

Abstract Monobodies are synthetic non-immunoglobulin customizable protein binders invaluable to basic and applied research, and of considerable potential as future therapeutics and diagnostic tools. The ability to reversibly control their binding activity to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, the development of a light-controlled monobody (OptoMB) that works in vitro and in cells and whose affinity for its SH2-domain target exhibits a 330-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. By virtue of their ability to be designed to bind any protein of interest, OptoMBs have the potential to find new powerful applications as light-switchable binders of untagged proteins with the temporal and spatial precision afforded by light.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Higher-order kinematical effects in deeply virtual Compton scattering

We study the deeply virtual Compton scattering cross-section in twist-two generalized parton distribution (GPD) approximation, and show that different choices of light-cone vectors and gauges for the final photon polarization will lead to different higher-order kinematical corrections to the cross-section formula. The choice of light-cone vectors affects kinematic corrections at the twist-three level, accounting for the differences between the cross-section formulas in the literature. On the other hand, kinematical corrections from higher-twist GPDs should eliminate the light-cone dependence at twist three. Those light-cone dependencies are studied systematically at JLab 12 GeV and future EIC kinematics. They serve as the intrinsic systematic uncertainties in extracting the Compton form factors through the cross-section formula. More importantly, they are also necessary for understanding cross-section measurements with higher-twist precision and to reconstruct higher-order Compton form factors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Quantum efficiency of InGaN–GaN multi-quantum well solar cells: Experimental characterization and modeling

InGaN-based multi-quantum well (MQW) solar cells are promising devices for photovoltaics (e.g., for tandem solar cells and concentrator systems), space applications, and wireless power transfer. In order to improve the efficiency of these devices, the factors limiting their efficiency and stability must be investigated in detail. Due to the complexity of a MQW structure, compared with a simple pn junction, modeling the spectral response of these solar cells is not straightforward, and ad hoc methodologies must be implemented. In this paper, we propose a model, based on material parameters and closed-formula equations, that describes the shape of the quantum efficiency of InGaN/GaN MQW solar cells, by taking into account the layer thickness, the temperature dependence of the absorption coefficient, and quantum confinement effects. We demonstrate (i) that the proposed model can effectively reproduce the spectral response of the cells; in addition, (ii) we prove that the bulk p-GaN layer absorbs radiation, but the carriers photogenerated in this region do not significantly contribute to device current. Finally, we show that (iii) by increasing the temperature, there is a redshift of the absorption edge due to bandgap narrowing, which can be described by Varshni law and is taken into account by the model, and a lowering in the extraction efficiency due to the increase in recombination (mostly Shockley–Read–Hall) inside the quantum wells, which is also visible by decreasing light intensity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Ab initio electroweak corrections to superallowed β decays and their impact on V ud

Radiative corrections are essential for an accurate determination of V ud from superallowed β decays. In view of recent progress in the single-nucleon sector, the uncertainty is dominated by the theoretical description of nucleus-dependent effects, limiting the precision that can currently be achieved for V ud . In this work, we provide a detailed account of the electroweak corrections to superallowed β decays in effective field theory (EFT), including the power counting, potential and ultrasoft contributions, and factorization in the decay rate. Here, we present a first numerical evaluation of the dominant corrections in light nuclei based on quantum Monte Carlo methods, confirming the expectations from the EFT power counting. Finally, we discuss strategies how to extract from data the low-energy constants that parametrize short-distance contributions and whose values are not predicted by the EFT. Combined with advances in ab initio nuclear-structure calculations, this EFT framework allows one to systematically address the dominant uncertainty in V ud , as illustrated in detail for the 14 O → 14 N transition.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Probing the Electronic Structure of Warm Dense Nickel via Resonant Inelastic X-Ray Scattering

The development of bright free-electron lasers (FEL) has revolutionized our ability to create and study matter in the high-energy-density (HED) regime. Current diagnostic techniques have been successful in yielding information on fundamental thermodynamic plasma properties, but provide only limited or indirect information on the detailed quantum structure of these systems, and on how it is affected by ionization dynamics. In this work we show how the valence electronic structure of solid-density nickel, heated to temperatures of around 10 of eV on femtosecond timescales, can be probed by single-shot resonant inelastic x-ray scattering (RIXS) at the Linac Coherent Light Source FEL. The RIXS spectrum provides a wealth of information on the HED system that goes well beyond what can be extracted from x-ray absorption or emission spectroscopy alone, and is particularly well suited to time-resolved studies of electronic-structure dynamics.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Capacitance Transients, Photoconductive Decay, and Impedance Spectroscopy on 19% to 22% Efficient Silicon Solar Cells

High efficiency silicon solar cells are characterized using current-voltage curves, electroluminescence imaging, impedance spectroscopy, capacitance transients, microwave photoconductive decay, and time-resolved photoluminescence imaging. The sample set is composed of cells from different manufacturers and includes an n-type silicon heterojunction (SHJ), an n-type passivated emitter rear totally diffused (PERT), and five different p-type passivated emitter rear contact (PERC) cells. Carrier lifetimes, both photoconductivity and photoluminescence, are measured co-located with the light excitation pulse and within the cell but away from the light spot. Luminescence intensity and excess carrier lifetimes correlate to cell voltage. The capacitance transient time constants correlate to the capacitance values extracted from impedance spectroscopy.

capacitance↗

DOE OSTI2025

Ultrafast renormalization of the magnetic continuum in the proximal Kitaev quantum spin liquid H 3 LiIr 2 O 6 by tr-RIXS [Invited]

We present the first circularly polarized non-resonant pump time-resolved resonant inelastic X-ray scattering (tr-RIXS) experiment in H 3 LiIr 2 O 6 , an iridium-based Kitaev system. Our calculations and experimental results are consistent with the modification of the low-energy magnetic excitations in H 3 LiIr 2 O 6 only during illumination by the laser pulse. We discuss these results in a cooperative framework between the Floquet engineering of the exchange interactions and the dynamic renormalization of electron-electron correlations. However, the penetration length mismatch between the X-ray probe and laser pump and the intrinsic complexity of Kitaev magnets prevents us from unequivocally extracting towards which ground state H 3 LiIr 2 O 6 is driven. We outline possible solutions to these challenges for light-driven stabilization and observation of the Kitaev quantum spin liquid limit by RIXS.

Kim, Jungho [Argonne National Laboratory (ANL), Ar↗

DOE OSTI2023

Capacitance Transients, Photoconductive Decay, and Impedance Spectroscopy on 19% to 22% Efficient Silicon Solar Cells

capacitance↗

DOE OSTI2020

Recovering cavity effects in corrugated organic light emitting diodes

Cavity effects play an important role in determining the out-coupling efficiency of an OLED. By fabricating OLEDs on corrugated substrates, the waveguide and SPP modes can be extracted by diffraction. However, corrugation does not always lead to an enhancement in out-coupling efficiency due to the reduction of the electrode reflectance and hence the cavity effects. Based on the results of our rigorous couple-wave analysis (RCWA) simulation, we found that the cavity effects can be partially recovered using a low index Teflon layer inserted between the ITO anode and the substrate due to the enhancement of the reflectance of the corrugated electrodes. To verify the simulation results, we fabricated corrugated OLEDs having a low-index Teflon interlayer with an EQE of 36%, which is 29% higher than an optimized planar OLED. By experimentally measuring the OLED air mode dispersion, we confirm the cavity emission of a corrugated OLED is enhanced by the low index layer.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Off-shell pion properties: Electromagnetic form factors and light-front wave functions

The off-shell pion electromagnetic form factors are explored with corresponding off-shell light-front wave functions modeled by constituent quark and antiquark. We apply the Mandelstam approach for the microscopic computation of the form factors relating the model parameters with the pion decay constant and charge radius. Analyzing the existing data on the cross sections for the Sullivan process, 1 H(e,e',π + )⁢n, Charged pion form factor between Q 2 = 0.60, and 2.45 GeV 2 . I. Measurements of the cross section for the 1 H⁡(e,e'⁢π + )⁢n reaction, we extract the off-shell pion form factor using the relation derived from the generalized Ward-Takahashi identity for the pion electromagnetic current. They are compared with our previous results from exactly solvable manifestly covariant model of a (3+1)-dimensional fermion field theory. We find that the adopted constituent quark model reproduces the extracted off-shell form factor F 1 ⁡(Q 2 ,t) from the experimental data within a few percent difference and matches well with our previous theoretical simulation which exhibits a variation of about 10% for the extracted off-shell pion form factor g(Q 2 ,t). We also identify the pion valence parton distribution function (PDF) and transverse momentum distribution (TMD) in terms of the light-front wave function and discuss their off-shell properties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1981

Fumigation of Alcohol in a Light Duty Automotive Diesel Engine

A light-duty automotive Diesel engine was fumigated with methanol in amounts up to 35% and 50% of the total fuel energy respectively in order to determine the effect of alcohol fumigation on engine performance at various operating conditons. Engine fuel efficiency, emissions, smoke, and the occurrence of severe knock were the parameters used to evaluate performance. Raw exhaust particulate and its soluble organic extract were screened for biological activity using the Ames Salmonella typhimurium assay. Results are given for a test matrix made up of twelve steady-state operating conditions. For all conditions except the 1/4 rack (light load) condition, modest thermal efficiency gains were noted upon ethanol fumigation. Methanol showed the same increase at 3/4 and full rack (high load) conditions. However, engine roughness or the occurrence of severe knock limited the maximum amount of alcohol that could be fumigated. Brake specific nitrogen oxide concentrations were found to decrease for all ethanol conditions tested. Oxides of nitrogen emissions, on a volume basis, decreased for all alcohol conditions tested. Based on the limited particulate data analyzed, it appears that ethanol fumigation, like methanol fumigation, while lowering the mass of particulated emitted, does enhance the biological activity of that particulate.

Broukhiyan, E. M. H.↗

DOE OSTI2021

Mechanism and kinetics of light alkane dehydrogenation and cracking over isolated Ga species in Ga/H-MFI

The objective of this study is to examine the mechanisms and kinetics of C2H6 dehydrogenation and n-C4H10 dehydrogenation and cracking over isolated Ga species in Ga/HMFI and to compare these results to those reported previously for C3H8 dehydrogenation and cracking. C2H6 dehydrogenation is found to be catalyzed by both [GaH]2+ and [GaH2]+ cations at similar turnover frequencies. Rate measurements over Ga/H-MFI containing predominantly [GaH2]+ cations reveal that C2H6 dehydrogenation rates exhibit a Langmuir.Hinshelwood dependence on C2H6 partial pressure at elevated temperatures (>730 K), consistent with the involvement of chemisorbed [C2H5.GaH]+ species. The reaction kinetics suggest that C2H6 dehydrogenation proceeds via heterolytic C-H cleavage of adsorbed C2H6 by [GaH2]+ cations to form H2 and [C2H5-GaH]+ species, which further decompose via β-hydride elimination to form C2H4. By contrast, C4H10 dehydrogenation and both terminal and central cracking are catalyzed exclusively by [GaH]2+ cations. All three reactions exhibit a Langmuir-Hinshelwood dependence on C4H10 partial pressure and are inhibited by H2. Ratios of dehydrogenation to cracking (total) and terminal to central cracking are approximately independent of C4H10 partial pressure consistent with the involvement of a common C4H10-derived surface intermediate. The observed reaction kinetics are consistent with an alkyl-mediated mechanism occurring over [GaH]2+, analogous to that reported previously for C3H8 dehydrogenation/cracking over Ga/H-MFI (Phadke, N. M.; et al. J. Am. Chem. Soc. 2019, 141, 1614-1627). The mechanism proceeds via facile, heterolytic dissociation of adsorbed C4H10 to form [C4H9-GaH]+-H+ cation pairs via methyl C-H-activated pathways. Dehydrogenation then proceeds via β-hydride elimination, respectively, forming butene, while terminal and central cracking proceed via C-H-activated H+ attack. Methylene activation was also considered but found to occur at a significantly lower rate. Theoretical analysis of the proposed reaction pathways leads to apparent activation enthalpies in good agreement with values extracted from the measured kinetics, thereby supporting the proposed pathways and the roles of [GaH]2+ and [GaH2]+ cations in the dehydrogenation and cracking of light alkanes on Ga/H-MFI.

Phadke, NM↗

NASA NTRS2014

A Framework for Land Cover Classification Using Discrete Return LiDAR Data: Adopting Pseudo-Waveform and Hierarchical Segmentation

Acquiring current, accurate land-use information is critical for monitoring and understanding the impact of anthropogenic activities on natural environments.Remote sensing technologies are of increasing importance because of their capability to acquire information for large areas in a timely manner, enabling decision makers to be more effective in complex environments. Although optical imagery has demonstrated to be successful for land cover classification, active sensors, such as light detection and ranging (LiDAR), have distinct capabilities that can be exploited to improve classification results. However, utilization of LiDAR data for land cover classification has not been fully exploited. Moreover, spatial-spectral classification has recently gained significant attention since classification accuracy can be improved by extracting additional information from the neighboring pixels. Although spatial information has been widely used for spectral data, less attention has been given to LiDARdata. In this work, a new framework for land cover classification using discrete return LiDAR data is proposed. Pseudo-waveforms are generated from the LiDAR data and processed by hierarchical segmentation. Spatial featuresare extracted in a region-based way using a new unsupervised strategy for multiple pruning of the segmentation hierarchy. The proposed framework is validated experimentally on a real dataset acquired in an urban area. Better classification results are exhibited by the proposed framework compared to the cases in which basic LiDAR products such as digital surface model and intensity image are used. Moreover, the proposed region-based feature extraction strategy results in improved classification accuracies in comparison with a more traditional window-based approach.

Light Detection & Ranging (LIDAR)↗

DOE OSTI2020

Characterization and recovery of rare earth elements and other critical metals (Co, Cr, Li, Mn, Sr, and V) from the calcination products of a coal refuse sample

Here, the impacts of calcination on the leaching recovery of rare earth elements (REEs) and other critical metals from a Baker seam coal refuse material were investigated. Acid leaching test results showed that leaching recovery of the REEs, especially the light REEs, was increased significantly from around 24% to 80–90% after calcination under 600–750 °C for two hours. By considering the major element leaching kinetics and the mineralogical changes of the dominant minerals caused by calcination, two mechanisms were proposed for the improved leaching performance: (1) decomposition of difficult-to-dissolve REE-bearing minerals into soluble forms; and (2) liberation of REE-bearing minerals encapsulated in clays after calcination due to the dehydration and disintegration of the layered clay structure. Sequential chemical extraction tests showed that a significant fraction (around 75%) of the REEs in the raw material were present in an insoluble form. After calcination under proper temperatures (600–800 °C), the majority of the insoluble light REEs (LREEs) were converted into soluble forms. Changes in the modes of occurrence of the LREEs and phosphorous based on leaching rate and sequential leaching correlated well as a function of the calcination temperature. This finding in addition to SEM-EDX results tends to indicate the potential that the LREEs occur primarily as rare earth phosphates such as monazite in the untreated coal refuse material. The acid leaching and sequential chemical extraction results show that co-extraction of REEs and other critical metals such as Co, Mn, and Li is possible using a calcination-acid leaching procedure.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2020

Subleading power resummation of rapidity logarithms: the energy-energy correlator in $ \mathcal{N} $ = 4 SYM

We derive and solve renormalization group equations that allow for the resummation of subleading power rapidity logarithms. Our equations involve operator mixing into a new class of operators, which we term the “rapidity identity operators”, that will generically appear at subleading power in problems involving both rapidity and virtuality scales. To illustrate our formalism, we analytically solve these equations to resum the power suppressed logarithms appearing in the back-to-back (double light cone) limit of the Energy-Energy Correlator (EEC) in $ \mathcal{N} $ = 4 super-Yang-Mills. These logarithms can also be extracted to $ \mathcal{O}\left({\alpha}_s^3\right) $ from a recent perturbative calculation, and we find perfect agreement to this order. Instead of the standard Sudakov exponential, our resummed result for the subleading power logarithms is expressed in terms of Dawson’s integral, with an argument related to the cusp anomalous dimension. We call this functional form “Dawson’s Sudakov”. Our formalism is widely applicable for the resummation of subleading power rapidity logarithms in other more phenomenologically relevant observables, such as the EEC in QCD, the p T spectrum for color singlet boson production at hadron colliders, and the resummation of power suppressed logarithms in the Regge limit.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗