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At least 1,117 records · Page 62

Integrated Biorefinery for Valorization of Engineered Bioenergy Crops—A Review

Biorefinery allows production of multiple bioproducts from various biomass and streams using suitable unit operations to improve the economics of process while minimizing waste generation. Biorefinery holds importance in the biofuel industry because multiple coproducts can allow to produce biofuels at a price which is competitive of fossil fuels. Newer generations of cellulosic biomasses are being developed to accumulate lipids and pigments. Such crops, which can be cultivated on land unsuitable for row crops, are aimed to provide drop-in fuels to reduce dependency on fossil fuels and food crops. This review describes the potential of recovery and value addition to different constituents of engineered crops besides producing drop-in fuels. As a result, the work also provides the market value of different products which can be obtained from engineered crops to make an informed decision.

09 BIOMASS FUELS↗

Automatic microseismic event picking via unsupervised machine learning

SUMMARY Effective and efficient arrival picking plays an important role in microseismic and earthquake data processing and imaging. Widely used short-term-average long-term-average ratio (STA/LTA) based arrival picking algorithms suffer from the sensitivity to moderate-to-strong random ambient noise. To make the state-of-the-art arrival picking approaches effective, microseismic data need to be first pre-processed, for example, removing sufficient amount of noise, and second analysed by arrival pickers. To conquer the noise issue in arrival picking for weak microseismic or earthquake event, I leverage the machine learning techniques to help recognizing seismic waveforms in microseismic or earthquake data. Because of the dependency of supervised machine learning algorithm on large volume of well-designed training data, I utilize an unsupervised machine learning algorithm to help cluster the time samples into two groups, that is, waveform points and non-waveform points. The fuzzy clustering algorithm has been demonstrated to be effective for such purpose. A group of synthetic, real microseismic and earthquake data sets with different levels of complexity show that the proposed method is much more robust than the state-of-the-art STA/LTA method in picking microseismic events, even in the case of moderately strong background noise.

Chen, Yangkang↗

Dust from evolved stars: a pilot analysis of the AGB to PN transition

ABSTRACT We present a novel approach to address dust production by low- and intermediate-mass stars. We study the asymptotic giant branch (AGB) phase, during which the formation of dust takes place, from the perspective of post-AGB and planetary nebula (PN) evolutionary stage. Using results from stellar evolution and dust formation modelling, we interpret the spectral energy distribution of carbon-dust-rich sources currently evolving through different evolutionary phases, believed to descend from progenitors of similar mass and chemical composition. Comparing the results of different stages along the AGB to PNe transition, we can provide distinct insights on the amount of dust and gas released during the very late AGB phases. While the post-AGB traces the history of dust production back to the tip of the AGB phase, investigating the PNe is important to reconstruct the mass-loss process experienced after the last thermal pulse. The dust surrounding the post-AGB was formed soon after the tip of the AGB. The PNe dust-to-gas ratio is ∼10−3, 2.5 times smaller than what expected for the same initial mass star during the last AGB interpulse, possibly suggesting that dust might be destroyed during the PN phase. Measuring the amount of dust present in the nebula can constrain the capacity of the dust to survive the central star heating.

Dell’Agli, F. (ORCID:0000000324426981)↗

The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes

Abstract G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3′-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5′-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.

59 BASIC BIOLOGICAL SCIENCES↗

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

59 BASIC BIOLOGICAL SCIENCES↗

Long-range quadrupole electron-phonon interaction from first principles

Lattice vibrations in materials induce perturbations on the electron dynamics in the form of long-range (dipole and quadrupole) and short-range (octopole and higher) potentials. The dipole Fröhlich term can be included in current first-principles electron-phonon (e-ph) calculations and is present only in polar materials. The quadrupole e-ph interaction is present in both polar and nonpolar materials, but currently it cannot be computed from first principles. In this work, we show an approach to compute the quadrupole e-ph interaction and include it in ab initio calculations of e-ph matrix elements. The accuracy of the approach is demonstrated by comparing with direct density functional perturbation theory calculations. We apply our method to silicon as a case of a nonpolar semiconductor and tetragonal PbTiO 3 as a case of a polar piezoelectric material. In both materials we find that the quadrupole term strongly impacts the e-ph matrix elements. Analysis of e-ph interactions for different phonon modes reveals that the quadrupole term mainly affects optical modes in silicon and acoustic modes in PbTiO 3 , although the quadrupole term is needed for all modes to achieve quantitative accuracy. The effect of the quadrupole e-ph interaction on electron scattering processes and transport is shown to be important. Our approach enables accurate studies of e-ph interactions in broad classes of nonpolar, polar, and piezoelectric materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Effect of iron redox ratio on the structures of boroaluminosilicate glasses

Iron oxide is commonly found in natural or industrial glass compositions and can exist as ferrous (Fe 2+ ) or ferric (Fe 3+ ) species, with their ratios depending on glass composition, temperature, pressure and the redox reactions during the glass forming process. The iron redox ratio plays an important role on silicate glass structures and consequently various properties. This work aims to study the effect of iron oxide, and particularly the iron redox ratio, on the structures of borosilicate and boroaluminosilicate glasses using molecular dynamics simulations with newly developed iron potential parameters that are compatible with the borosilicate potentials. The results provide detailed cation coordination states of both iron species and the effect of redox ratio on boron coordination and other structural features. Particularly, competition for charge compensating modifier cations (such as Na + ) among the fourfold-coordinated cations such as B 3+ , Al 3+ , and Fe 3+ is investigated by calculating the cation–cation pair distribution functions and coordination preferential ratios. The results show that the trivalent ferric ions, with a shorter Fe–O bond distance and better defined first coordiation shell with mainly four-fold coordination, act as a glass former whereas the divalent ferrous ions mainly play the role of glass modifier. The ferrous/ferric ratio (Fe 2+ /Fe 3+ ) was found to affect the glass chemistry and hence glass properties by regulating the amount of four-coordinated boron, the fraction of non-briding oxygen and other features. Finally, the results are compared with available experimental data to gain insights of the complex structures and charge compensation schemes of the glass system.

36 MATERIALS SCIENCE↗

Jasmonate activates secondary cell wall biosynthesis through MYC2–MYB46 module

Formation of secondary cell wall (SCW) is tightly regulated spatiotemporally by various developmental and environmental signals. Successful fine-tuning of the trade-off between SCW biosynthesis and stress responses requires a better understanding of how plant growth is regulated under environmental stress conditions. However, the current understanding of the interplay between environmental signaling and SCW formation is limited. The lipid-derived plant hormone jasmonate (JA) and its derivatives are important signaling components involved in various physiological processes including plant growth, development, and abiotic/biotic stress responses. Recent studies suggest that JA is involved in SCW formation but the signaling pathway has not been studied for how JA regulates SCW formation. We tested this hypothesis using the transcription factor MYB46, a master switch for SCW biosynthesis, and JA treatments. Both the transcript and protein levels of MYB46, a master switch for SCW formation, were significantly increased by JA treatment, resulting in the upregulation of SCW biosynthesis. We then show that this JA-induced upregulation of MYB46 is mediated by MYC2, a central regulator of JA signaling, which binds to the promoter of MYB46. We conclude that this MYC2-MYB46 module is a key component of the plant response to JA in SCW formation.

59 BASIC BIOLOGICAL SCIENCES↗

Beam Hardening Artifact Reduction in X-Ray CT Reconstruction of 3D Printed Metal Parts Leveraging Deep Learning and CAD Models

Nondestructive evaluation (NDE) of additively manufactured (AM) parts is important for understanding the impacts of various process parameters and qualifying the built part. X-ray computed tomography (XCT) has played a critical role in rapid NDE and characterization of AM parts. However, XCT of metal AM parts can be challenging because of artifacts produced by standard reconstruction algorithms as a result of a confounding effect called “beam hardening.” Beam hardening artifacts complicate the analysis of XCT images and adversely impact the process of detecting defects, such as pores and cracks, which is key to ensuring the quality of the parts being printed. In this work, we propose a novel framework based on using available computer-aided design (CAD) models for parts to be manufactured, accurate XCT simulations, and a deep-neural network to produce high-quality XCT reconstructions from data that are affected by noise and beam hardening. Using extensive experiments with simulated data sets, we demonstrate that our method can significantly improve the reconstruction quality, thereby enabling better detection of defects compared with the state of the art. We also present promising preliminary results of applying the deep networks trained using CAD models to experimental data obtained from XCT of an AM jet-engine turbine blade.

Ziabari, Amir↗

Highly selective Si 3 N 4 /SiO 2 etching using an NF 3 /N 2 /O 2 /H 2 remote plasma. II. Surface reaction mechanism

Developing processes for highly selective etching of silicon nitride (Si 3 N 4 ) with respect to silicon dioxide (SiO 2 ) is a major priority for semiconductor fabrication processing. In this paper and in Paper I [Volynets et al., J. Vac. Sci. Technol. A 38, 023007 (2020)], mechanisms are discussed for highly selective Si3N4 etching in a remote plasma based on experimental and theoretical investigations. The Si 3 N 4 /SiO 2 etch selectivity of up to 380 was experimentally produced using a remote plasma sustained in NF 3 /N 2 /O 2 /H 2 mixtures. A selectivity strongly depends on the flow rate of H 2 , an effect attributed to the formation of HF molecules in vibrationally excited states that accelerate etching reactions. Based on experimental measurements and zero-dimensional plasma simulations, an analytical etching model was developed for etch rates as a function of process parameters. Reaction rates and sticking coefficients were provided by quantum chemistry models and also fitted to the experimental results. Etch rates from the analytical model show good agreement with the experimental results and demonstrate why certain etchants accelerate or inhibit the etch process. In particular, the modeling shows the important role of HF molecules in the first vibrationally excited state [HF( v = 1)] in achieving high Si 3 N 4 /SiO 2 selectivity.

42 ENGINEERING↗

Application of automated iterative target detection for standoff hyperspectral imaging

The utility of hyperspectral imaging (HSI) has been well established for a wide array of applications but has generated a need for automated screening of high volumes of large HSI cubes. We report two important automated algorithms for more efficient standoff processing: atmospheric correction and target detection. The atmospheric correction method is based on a fast asymmetric least squares approach that is applied on a pixel-by-pixel basis. Here, the correction can be applied to entire images without manually identifying regions of interest and utilizes only in-scene information, no ancillary modeling of the atmosphere is required. An iterative target detection approach is also introduced which demonstrates faster speeds relative to moving window approaches. The target detection algorithm classifies each pixel as true target detections, near target detections, clutter, and no-calls. The algorithms were tested on forty images of twenty-two solid mineral targets placed at a 14-meter standoff distance allowing general observations on expected detection performance for a variety of minerals. In addition to identifying anomalous pixels, the inclusion of “no-calls” reduced the number of false detections significantly.

47 OTHER INSTRUMENTATION↗

High grain boundary recombination velocity in polycrystalline metal halide perovskites

Understanding carrier recombination processes in metal halide perovskites is fundamentally important to further improving the efficiency of perovskite solar cells, yet the accurate recombination velocity at grain boundaries (GBs) has not been determined. Here, we report the determination of carrier recombination velocities at GBs (S GB ) of polycrystalline perovskites by mapping the transient photoluminescence pattern change induced by the nonradiative recombination of carriers at GBs. Charge recombination at GBs is revealed to be even stronger than at surfaces of unpassivated films, with average S GB reaching 2200 to 3300 cm/s. Regular surface treatments do not passivate GBs because of the absence of contact at GBs. We find a surface treatment using tributyl(methyl)phosphonium dimethyl phosphate that can penetrate into GBs by partially dissolving GBs and converting it into one-dimensional perovskites. It reduces the average S GB by four times, with the lowest SGB of 410 cm/s, which is comparable to surface recombination velocities after passivation.

36 MATERIALS SCIENCE↗

Archaeosine Modification of Archaeal tRNA: Role in Structural Stabilization

Archaeosine is ubiquitous in archaeal tRNA, where it is located at position 15. Based on its molecular structure, it was proposed to stabilize tRNA, and we show that loss of archaeosine in Thermococcus kodakarensis results in a strong temperature-sensitive phenotype, while there is no detectable phenotype when it is lost in Methanosarcina mazei . Measurements of tRNA stability show that archaeosine stabilizes the tRNA structure but that this effect is much greater when it is present in otherwise unmodified tRNA transcripts than in the context of fully modified tRNA, suggesting that it may be especially important during the early stages of tRNA processing and maturation in thermophiles. Our results demonstrate how small changes in the stability of structural RNAs can be manifested in significant biological-fitness changes.

Microbiology↗

Clumped isotope constraints on changes in latest Pleistocene hydroclimate in the northwestern Great Basin: Lake Surprise, California

Abstract During the Last Glacial Maximum (LGM) and subsequent deglaciation, the Great Basin in the southwestern United States was covered by numerous extensive closed-basin lakes, in stark contrast with the predominately arid climate observed today. This transition from lakes in the Late Pleistocene to modern aridity implies large changes in the regional water balance. Whether these changes were driven by increased precipitation rates due to changes in atmospheric dynamics, decreased evaporation rates resulting from temperature depression and summer insolation changes, or some combination of the two remains uncertain. The factors contributing to these large-scale changes in hydroclimate are critical to resolve, given that this region is poised to undergo future anthropogenic-forced climate changes with large uncertainties in model simulations for the 21st century. Furthermore, there are ambiguous constraints on the magnitude and even the sign of changes in key hydroclimate variables between the Last Glacial Maximum and the present day in both proxy reconstructions and climate model analyses of the region. Here we report thermodynamically derived estimates of changes in temperature, precipitation, and evaporation rates, as well as the isotopic composition of lake water, using clumped isotope data from an ancient lake in the northwestern Great Basin, Lake Surprise (California). Compared to modern climate, mean annual air temperature at Lake Surprise was 4.7 °C lower during the Last Glacial Maximum, with decreased evaporation rates and similar precipitation rates to modern. During the mid-deglacial period, the growth of Lake Surprise implied that the lake hydrologic budget briefly departed from steady state. Our reconstructions indicate that this growth took place rapidly, while the subsequent lake regression took place over several thousand years. Using models for precipitation and evaporation constrained from clumped isotope results, we determine that the disappearance of Lake Surprise coincided with a moderate increase in lake temperature, along with increasing evaporation rates outpacing increasing precipitation rates. Concomitant analysis of proxy data and climate model simulations for the Last Glacial Maximum are used to provide a robust means to understand past climate change, and by extension, predict how current hydroclimates may respond to expected future climate forcings. We suggest that an expansion of this analysis to more basins across a larger spatial scale could provide valuable insight into proposed climate forcings, and aid in climate model process depiction. Ultimately, our analysis highlights the importance of temperature-driven evaporation as a mechanism for lake growth and retreat in this region.

Geology↗

Hydration Mimicry by Membrane Ion Channels

Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if these protein channels provide environments similar to the aqueous solution hydration environment. In fact, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry concept depends on understanding the hydration structure and free energies of metal ions in water in order to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water and the molecular quasi-chemical theory that provides hydration free energies. In doing so, we note some current views of ion binding to membrane channels and suggest new physical chemical calculations and experiments that might further clarify the hydration mimicry concept.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Macro-physical Properties of Shallow Cumulus from Integrated ARM Observations (Final Report)

Fair-weather shallow cumuli (ShCu) play an important role in many climate-related processes. Irregular geometry of ShCu and their strong temporal and spatial variability make it challenging to observe ShCu holistically and to represent them correctly in climate models. To improve ShCu parameterizations, information on both vertically and horizontally resolved cloud properties is required. Commonly, the vertically resolved cloud properties are provided by zenith pointing lidar-radar observations with a very narrow field of view (FOV). Thus, these “pencil-beam” properties may not be representative of a larger surrounding area. Limited number of areal-averaged cloud properties, such as fractional sky cover (FSC), are offered typically by wide-FOV observations. The main goal of our project was to integrate advantages of the narrow-FOV (vertical structure of clouds) and wide-FOV (spatial arrangement of clouds) observations for an improved characterization of single-layer ShCu observed at the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site for an 18-yr period (2000-2017). There are four major accomplishments of our project, First, an updated operational cloud classification for days with ShCu has been suggested and evaluated through a detailed comparison with the manually curated records. Our classification extends successfully the latest ARM cloud type Value Added Product (VAP) based on the Active Remote Sensing of Clouds (ARSCL) cloud product by incorporating both cloud fraction (CF) provided by narrow-FOV ceilometer data and FSC from wide-FOV images offered by a Total Sky Imager (TSI). Moreover, our classification allows one to identify impact of instrumentation changes at the SGP site, namely the transition to KAZRARSCL with the updated cloud radar, on the identification of periods with single-layer ShCu. Second, a new approach that resolves cloud area distributions for a given region (up to 4x4 km 2 ) has been suggested and cloud equivalent diameters (CEDs) have been estimated for the first time. These estimations have been performed over a wide range of cloud sizes (about 0.01–3.5 km) with high temporal resolution (30s) using wide-FOV TSI images and cloud base height (CBH) provided by complementary narrow-FOV lidar measurements. Our simple and computationally inexpensive approach offers a previously unavailable dataset for process studies in the convective boundary layer and evaluation of ShCu parameterizations in cloud-resolving models. Third, a long-term integrated record of ShCu macrophysical properties has been developed. The developed record represents the longest available compilation of events with ShCu and includes (i) a novel visualization of the spatial variability in cloud cover both along- and across-wind directions, (ii) updated estimates of narrow-FOV CF and wide-FOV FSC, (iii) updated narrow-FOV CBH, and (iv) complementary data, such as wind speed and direction from the 915-MHz Radar Wind Profiler (RWP) data. The developed record has been used successfully to assess conventional observational estimates of cloud cover and their sensitivity to the following two factors: (i) instrument-dependent cloud detection and data merging criteria and (ii) FOV configuration. Fourth, co-variability of the ShCu macrophysical properties and environmental parameters has been analyzed for a 3-yr period (2016-2018). Our initial analysis includes diurnal changes of FSCs obtained for clouds with small, moderate and large CEDs and several environmental parameters, such as lifted condensation level (LCL) and mixed layer height (zi). Preliminary results of our analysis suggest that the horizontal extent of ShCu is controlled substantially by the sign and magnitude of difference between these two parameters (zi-LCL): the CED tends to grow with increase of this difference (zi exceeds LCL). We have initiated relationships between the ShCu and key atmospheric parameters that control both the development and evolution of ShCu using our new data product, which combines effectively the advantages of narrow-FOV data offered by zenith pointing cloud radars and lidars and wide-FOV TSI images. While the latest instrumentation at the ARM sites may address these challenging relationships in the future, we believe that the historical ARM data at the SGP site has not yet been fully utilized. Overall, our data product can be used by researchers working on a wide range of climate-related projects. These projects may include (i) a comprehensive evaluation of outputs from the Large-Eddy Simulation (LES) and single-column models for their future improvement, (ii) the representativeness of “short-period” results obtained from the previous model and observational studies and (iii) the planning of future field campaigns with focus on improved understanding of the diurnal cycle of cumulus convection.

54 ENVIRONMENTAL SCIENCES↗

Development of Large Scale Extrusion Deposition for Structural Applications

Large Scale Extrusion Deposition (LSED) is an evolving additive manufacturing (AM) technology that research, such as that taking place at Oak Ridge National Laboratory (ORNL) and companies like Local Motors, are continuing to utilize and develop new applications. A major LSED application of interest has been molds and tooling as it allows for much shorter production time and lower cost. However, interest has been expanding into using LSED for more structural applications due to more frequent use of high performing polymer composites as feedstock. The use of LSED for structural applications is of particular interest to Local Motors as it is currently being used to create commercially viable, energy efficient electric vehicles. LSED offers a unique opportunity when compared to traditional manufacturing methods as it can significantly reduce the number of components necessary, while decreasing embodied energy and carbon emissions. Even with these benefits however, it is important that LSED is properly understood from a structural aspect as this field has not been as heavily researched as tooling. To ensure a high level of safety and repeatability is an essential responsibility of a manufacturer whose products are structural in nature. As such it is important to understand the materials and LSED process to make structural objects that the manufacturer can be confident in. The main goals of this project were to: develop and investigate materials that are of interest for structural LSED applications, further develop and understand the current machines used in LSED and develop simulations tools of LSED and the mechanical properties of the created structure. Material development focused on composite materials that have high mechanical properties and are stable in a variety of environments. The materials were tested to determine their as printed mechanical and thermal properties as these are necessary for simulations. Once the materials were investigated thoroughly, it allowed for simulations to be performed to compare to experimental data with simulations. Materials were also vetted to determine candidates for multi-material printing. The machine development focused around the areas of process monitoring, non-destructive evaluation, and quality control. Finally, the goal of the simulations was to develop a realistic model of printed structures, including in-process simulation and dynamic simulation. The routes to get to some of these goals and the depth in which they were investigated changed throughout the project due to personnel changes and the COVID-19 pandemic. This project resulted in many valuable results such as the development of an nondestructive evaluation (NDE) technique for interlayer defects, proof of simulation for warpage in simple parts, the development and utilization of a profilometer to monitor a print for defects or inconsistencies, thorough investigation of a material used commercially for structural LSED applications and valuable experimental data on the applicability and advantages of multi-material crush structures versus their neat counterparts by creation and testing of samples.

36 MATERIALS SCIENCE↗

Chlorine Worth Study in Support of PF-4 Operations [Slides]

Aqueous Chloride Operations at PF-4 are important because they recover Pu from other processes, reduce waste sent to WIPP, and increase throughput for Am production. Aqueous Chloride Operations have very conservative mass limits (~520 grams Pu) and significant amounts of Chlorine but calculations not crediting Cl-35 neutron absorption accounting for Cl-35 absorption leads to higher mass limits. Can experiments be designed/conducted to provide technical justification to NCS in order to increase mass limits?

2019 ARCHIMEDES LDRD project↗