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NASA NTRS2001

Effects of exposure to 56Fe particles on the acquisition of a conditioned place preference in rats

Exposure to low doses of 56Fe particles produces changes in neural function and behavior. The present experiments were designed to examine the effects of irradiation on the acquisition of a dopamine-mediated conditioned place preference (CPP). In the CPP procedure, rats are given an injection of the dopamine agonist amphetamine in one distinctive compartment and a saline injection in a different compartment of a three-compartment apparatus. Control rats develop a preference for the amphetamine-paired compartment. In contrast, rats exposed to 1 Gy of 56Fe particles fail to develop a similar preference. The results of the experiment indicate that exposure to low doses of heavy particles can disrupt the neural mechanisms that mediate the reinforcement of behavior.

Non-NASA Center↗

DOE OSTI2022

Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager’s activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2004

Note on the Effect of Horizontal Gradients for Nadir-Viewing Microwave and Infrared Sounders

Passive microwave and infrared nadir sounders such as the Advanced Microwave Sounding Unit A (AMSU-A) and the Atmospheric InfraRed Sounder (AIRS), both flying on NASA s EOS Aqua satellite, provide information about vertical temperature and humidity structure that is used in data assimilation systems for numerical weather prediction and climate applications. These instruments scan cross track so that at the satellite swath edges, the satellite zenith angles can reach approx. 60 deg. The emission path through the atmosphere as observed by the satellite is therefore slanted with respect to the satellite footprint s zenith. Although radiative transfer codes currently in use at operational centers use the appropriate satellite zenith angle to compute brightness temperature, the input atmospheric fields are those from the vertical profile above the center of the satellite footprint. If horizontal gradients are present in the atmospheric fields, the use of a vertical atmospheric profile may produce an error. This note attempts to quantify the effects of horizontal gradients on AIRS and AMSU-A channels by computing brightness temperatures with accurate slanted atmospheric profiles. We use slanted temperature, water vapor, and ozone fields from data assimilation systems. We compare the calculated slanted and vertical brightness temperatures with AIRS and AMSU-A observations. We show that the effects of horizontal gradients on these sounders are generally small and below instrument noise. However, there are cases where the effects are greater than the instrument noise and may produce erroneous increments in an assimilation system. The majority of the affected channels have weighting functions that peak in the upper troposphere (water vapor sensitive channels) and above (temperature sensitive channels) and are unlikely t o significantly impact tropospheric numerical weather prediction. However, the errors could be significant for other applications such as stratospheric analysis. Gradients in ozone and tropospheric temperature appear to be well captured by the analyses. In contrast, gradients in upper stratospheric and mesospheric temperature as well as upper tropospheric humidity are less well captured. This is likely due in part to a lack of data to specify these fields accurately in the analyses. Advanced new sounders, like AIRS, may help to better specify these fields in the future.

Joiner, J.↗

NASA NTRS1950

Theoretical Investigation of a Proportional-Plus-Flicker Automatic Pilot

The proportional-plus-flicker automatic pilot operates by a nonlinear principle whereby a fast-acting flicker servomotor response is combined with a low-speed proportional servomotor response for the purpose of obtaining supersonic stability and control. Essentially, the autopilot maintains a zero reference about which the output is proportional to the input. However, a flicker response overrides this proportional response at a fixed angle of gimbal displacement on either side of the zero gyroscope reference. Therefore, in contrast to other high speed control systems, the design requirements are simplified because the two components of the proportional-flicker control system are easy to build separately and they can be combined in a relatively simple manner. By application of the proportional-flicker principle, satisfactory stability can be obtained by the proper adjustment of the variable factors in the autopilot mechanism; namely, the proportional gain, the amplitude of flicker control deflection, the autopilot time-lag factor (the time-lag between flicker and proportional operation), and the point in the range that the autopilot switches from a flicker to a proportional system. There is a possibility that these factors can be adjusted so that a more rapid response time (the time to reach steady state) is obtained with the non-linear proportional-flicker autopilot than with a purely linear proportional autopilot. For the main part of this analysis, the proportional part of the system is approximated by a zero-phase-lag proportional autopilot with the assumption that the control surface moves instantaneously at the point where the system switches from flicker to proportional. Good correlation is shown between the results obtained by this method and results obtained by using a close approximation of an actual autopilot transfer function for proportional autopilot operation.

Seaberg, Ernest C.↗

DOE OSTI2020

Distonic radical anion species in cysteine oxidation processes

Oxidation of cysteine residues constitutes an important regulatory mechanism in the function of biological systems. Much of this behavior is controlled by the specific chemical properties of the thiol side-chain group, where reac-tions with reactive oxygen species take place. Herein, we in-vestigated the entire cysteine oxidation cycle Cys-SH ? Cys-SOnH (n = 1, 2, 3) using cryogenic negative ion photoelectron spectroscopy and quantum-chemical calculations. The conven-tional view on the first reversible oxidation step (n = 1) is as-sociated with sulfinate species. Yet our results indicate that an alternative option exists in the form of novel distonic radical anion •OS-CH2CH(NH2)-COO- with an unpaired electron on the thiol group and excess negative charge on the carboxylate. Higher order oxidation states (n = 2, 3) are thought to be asso-ciated with irreversible oxidative damage, and our results show that excess negative charge in those cases migrates to -SOn- group. Furthermore, these species are stable towards 1e oxidation, as opposed to the n = 1 case that undergoes intra-molecular proton transfer. The molecular level insights report-ed in this work provide direct spectroscopic evidences towards unique chemical versatility of Cys-sulfenic acid (Cys-SOH) in post-translational modifications of protein systems. This research was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences (X.-B. W. and M. V.) and was performed at the EMSL, a national scientific user facility sponsored by DOE's Office of Biological and Environmental Research and located at the Pacific Northwest National Laboratory. Z. B. Q. acknowledges additional support from the National Natural Science Foundation of China (Grant No. 21873003 and 21503003) and the Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase) (Grant No. U1501501) and Super Computation of Shenzhen.

Qin, Zhengbo↗

DOE OSTI2023

Electronic structure and energetics of a heterodimeric BChl g ′/Chl a ′ special pair generated by exposure of Heliomicrobium modesticaldum to dioxygen

Heliobacteria are anoxygenic phototrophs that have a Type I homodimeric reaction center containing bacteriochlorophyll g (BChl g). Previous experimental studies have shown that in the presence of light and dioxygen, BChl g is converted into 8 1 -OH-chlorophyll a F (hereafter Chl a F ), with an accompanying loss of light-driven charge separation. These studies suggest that the reaction center only loses the ability to transfer electrons once both BChl g′ molecules of the P 800 special pair have been converted to Chl a F ′. Here, the present work confirms that the partially converted BChl g′/Chl a F ′ special pair remains functional in samples exposed to dioxygen by demonstrating its presence using hyperfine couplings obtained from Q-band 1 H ENDOR, 2D 14 N HYSCORE and DFT methods. The DFT calculations of the BChl g′/BChl g′ homodimeric primary donor, which are based on the recently published X-ray crystal structure, predict that the unpaired electron spin is equally delocalized over both BChl g′ molecules and provide an excellent match to the experimental hyperfine couplings of the anaerobic samples. Exposure to dioxygen leads to substantial changes in the hyperfine interactions, indicative of greater localization of the unpaired electron spin. The measured hyperfine couplings are reproduced in the DFT calculations by replacing one of the BChl g′ molecules of the primary donor with a Chl a F ′ molecule. The calculations reveal that the spin density becomes localized on BChl g′ in the heterodimeric primary donor. Time-dependent DFT calculations demonstrate that conversion of either or both of the accessory BChl g molecules and/or one of the BChl g′ molecules of P800 to Chl a F ′ results in minor effects on the energy of the charge-separated states. In contrast, if both of the BChl g′ molecules of P 800 are converted a large increase in the energy of the charge-separated state occurs. This suggests that the reaction center remains functional when only one half of the dimer is converted, however, conversion of both halves of the P 800 dimer leads to loss of function

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Electron Spin Polarization and Rectification Driven by Chiral Perylene Diimide-Based Nanodonuts

The chirality-induced spin selectivity (CISS) effect allows thin-film layers of chiral conjugated molecules to function as spin filters at ambient temperature. Through solvent-modulated dropcasting of chiral l- and d-perylene diimide (PDI) monomeric building blocks, two types of aggregate morphologies, nanofibers and nanodonuts, may be realized. Spin-diode behavior is evidenced in the nanodonut structures. Stacked PDI units, which form the conjugated core of these nanostructures, dominate the nanodonut–Au electrode contact; in contrast, the AFM tip contacts largely the high-resistance solubilizing alkyl chains of the chiral monomers that form these nanodonuts. Current–voltage responses of the nanodonuts, measured by magnetic conductive AFM (mC-AFM), demonstrate substantial spin polarizations as well as spin current rectification ratios (>10) that exceed the magnitudes of those determined to date for other chiral nanoscale systems. Furthermore, these results underscore the potential for chiral nanostructures, featuring asymmetric molecular junctions, to enable CISS-based nanoscale spin current rectifiers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Single and dual metal atom catalysts for enhanced singlet oxygen generation and oxygen reduction reaction

We demonstrate rational design of graphene-supported single and dual metal atom catalysts (SACs and DACs) for photocatalytic applications, such as singlet oxygen ( 1 O 2 ) sensitization and H 2 O 2 production. Here we combine density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations with experimental verifications. We found a synergistic effect between triplet sensitization and triplet–triplet (Dexter) energy transfer; both play a role in the photocatalytic activity through the volcano plot of 3d transition metal SACs. More specifically, FeN 4 -SAC exhibits a low ISC energy gap (ΔE ISC ) of 0.039 eV, compared with 0.108 eV for FeNiN8-DACs, both possessing a high Bader charge transfer of 0.366 e- and 0.405 e-, respectively. Guided by these computational results, we synthesized a series of SACs and a DAC and confirmed their structures with scanning transmission electron microscopy (STEM) along with the X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). We then confirm their band structures with low-energy inverse photoemission spectroscopy (LEIPS) and UV-vis-NIR. Subsequently, we synthesized the catalysts for the photooxygenation of anthracene and two-electron oxygen reduction reaction (ORR) to measure their photocatalytic activity. We found that H 2 O 2 production through the two-electron ORR competes with the 1 O 2 generation through Dexter energy transfer. FeN 4 -SAC demonstrates a high photooxygenation conversion of 86% and a high 1 O 2 quantum yield of 1.04, obtained from electron spin resonance (ESR) spectroscopy, with low H 2 O 2 production. In contrast, NiN 4 -SAC exhibits a low 1 O 2 generation and a high H 2 O 2 production mainly because of the high Gibbs free energy of the OOH* intermediate. In conclusion, this work proposes an effective DFT-guided strategy for designing SACs and DACs for various photocatalytic applications.

36 MATERIALS SCIENCE↗

DOE OSTI2025

A variant of the MenB strain of Synechocystis sp. PCC 6803 disrupts a stress response pathway allowing DMPBQ to occupy the A 1 sites of photosystem I

Phylloquinone (PhQ) plays a unique role in photosynthesis as the A1A and A1B intermediates in light-driven electron transfer in Photosystem I (PSI). When PhQ biosynthesis is inhibited by deletion of the menB gene in the cyanobacterium Synechocystis sp. PCC 6803, previous studies have shown that plastoquinone-9 (PQ-9) occupies the A 1 sites. However, a recent cryo-electron microscopy structure of a strain of ΔmenB from the year 2023 revealed an unusual quinone in the A 1 sites with a benzoquinone headgroup similar to PQ-9 and a phytyl tail similar to PhQ. Here, we investigate its biosynthesis and binding properties. Mass spectrometry confirms that PSI from the 2023 ΔmenB strain contains 2,3-dimethyl-5-phytyl-1,4-benzoquinone (DMPBQ), while PSI from the original strain contains PQ-9. Whole genome sequencing reveals that a mutation in slr1737 (tocopherol cyclase) leads to the accumulation of DMPBQ, an intermediate in the tocopherol biosynthetic pathway. Transient optical and electron paramagnetic resonance spectroscopy studies show that when DMPBQ occupies the A 1 sites, it does not exchange with exogenously supplied PhQ in contrast to PQ-9, which exchanges readily. We propose that the slr1737 mutation in the 2023 ΔmenB strain is a likely candidate for the source of the phenotype. This new strain has sacrificed tocopherol synthesis, the absence of which is known to have no effect on growth under low stress conditions, resulting in incorporation of DMPBQ in the A 1 sites. The tighter binding and function of DMPBQ likely allow this ΔmenB strain to outcompete its peers under optimal growth conditions and thus dominate the population.

2,3-dimethyl-5-phytyl-1,4-benzoquinone↗

DOE OSTI2026

Arabidopsis cytochrome b 5 proteins support fatty acid ω-3 but not ω-6 desaturation

Fatty acids are primary components of lipids, which serve as major energy sources in cells and play essential roles in membrane structure, signaling, and metabolic regulation (Shanklin and Cahoon 1998). The degree of fatty acid unsaturation critically influences lipid physicochemical properties, thereby affecting membrane fluidity and biological function (Nguyen et al. 2019). In Arabidopsis thaliana, fatty acid desaturation occurs via 2 parallel pathways: the “prokaryotic pathway” in plastids, involving glycosylglycerides, such as monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), and phospholipid phosphatidylglycerol (PG); and the “eukaryotic pathway” in the endoplasmic reticulum (ER), involving phosphatidylcholine (PC) (Lou et al. 2014) (Supplementary Figure S1). Seven fatty acid desaturases (FADs) in Arabidopsis differentially desaturate each glycerolipid class in the plastid and ER (Nguyen et al. 2019). FAD2, an ER-resident ω-6 fatty acid desaturase, catalyzes the conversion of oleic acid (18:1) to linoleic acid (18:2), which can be further desaturated to α-linolenic acid (18:3) by FAD3, an ER-resident ω-3 fatty acid desaturase. In plastids, FAD6 catalyzes the desaturation of 18:1/16:1 to produce 18:2/16:2, while FAD7 and FAD8 redundantly convert 18:2/16:2 to 18:3/16:3 (Li-Beisson et al. 2013; Nguyen et al. 2019). Additionally, fatty acids synthesized in the ER can also be reimported into plastids to their site of de novo synthesis (Xu et al. 2010). All FADs require reducing power, in the form of 2 electrons, for catalysis, but the sources of the electrons vary between their subcellular localizations. In the ER, FAD2 and FAD3 receive electrons from a cytochrome b 5 (CB5)-based electron transfer chain comprising cytochrome b 5 reductase (CBR) and CB5. In contrast, ferredoxin serves as the electron donor for plastid-localized FAD6, FAD7, and FAD8 (Ohlrogge and Browse 1995; Andreu et al. 2007). While the relative contributions of the 2 pathways to total cellular desaturation products vary across tissues and species, most polyunsaturated FA biosynthesis in seeds occurs via ER-resident FAD2 and FAD3 (Miquel and Browse 1992; Ohlrogge and Browse 1995).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Ecological Insights from Transferable Plant Biomass Mapping across the Arctic using High-resolution Structure-from-Motion and LiDAR Data

Warmer temperatures, permafrost thaw, and increased wildfire activity are driving rapid ecological change across the Arctic, significantly altering plant productivity and aboveground biomass (AGB). These rapid changes highlight the urgent need to improve monitoring of vegetation dynamics in the Earth’s northern ecosystems, where high spatiotemporal heterogeneity occurs at scales finer than those captured by traditional satellite observations. The growing use of Unoccupied Aerial Systems (UASs) presents an opportunity to overcome this limitation. Yet, the diversity of UAS platforms, sensors, and data collection and processing workflows presents challenges for developing standardized, generalizable approaches. To address this challenge, we compiled 672 AGB plots co-located with 183 UAS-based Structure-from-Motion (SfM) or Light Detection and Ranging (LiDAR) surveys collected across the Arctic. Here, we: (1) evaluated the generalizability of UAS-derived canopy structure derived from high-resolution SfM and LiDAR for estimating AGB, (2) assessed scaling errors and their sources in two recent satellite-based AGB products derived from Landsat and MODIS, and (3) demonstrated the use of high-resolution AGB maps to quantify biomass variation across tundra plant functional types (PFTs) and to monitor post-fire recovery. Our results show that both SfM and LiDAR accurately captured AGB and its variability across tundra PFTs using a Random Forest (RF) model (overall RMSE: 0.336 kg/m2), with mapping performance varying slightly by region and data source. Using UAS-derived AGB maps as a benchmark, we identified systematic biases in satellite-derived AGB products, largely attributable to the magnitude of AGB and structural heterogeneity within coarse-resolution pixels. Applying our model to repeat UAS surveys following a tundra fire on Seward Peninsula, we observed rapid AGB recovery in non-shrub patches, with biomass recovering to pre-fire levels within 2 years. In contrast, shrub patches recovered more slowly, with AGB gains continuing over 2–4 years through both in-patch growth and lateral expansion (via dispersal) into remaining burned areas. Overall, these findings demonstrate the generalizability of UAS-based SfM and LiDAR data for estimating tundra AGB and highlight the potential of our approach to be broadly applied to generate high-quality AGB data for ecological monitoring and model benchmarking across the Arctic.

Yang, Daryl [ORNL] (ORCID:0000000317057823)↗

DOE OSTI2023

Revisiting the definition of field capacity as a functional parameter in a layered agronomic soil profile beneath irrigated maize

The soil water content at the condition of field capacity (θ FC ) is a key parameter in irrigation scheduling and has been suggested to be determined by running a synthetic drainage experiment until the flux rate (q) at the bottom of the soil profile achieves a predefined negligible value (q FC ). We question the impact of q FC on the assessment of field capacity. Moreover, calculating θ FC as the integral mean of the water content profile when q is equal to q FC is strictly valid only for uniform soil profiles. By contrast, this practice is ambiguous and biased for stratified soil profiles due to the soil water content discontinuity at the layer interfaces. In this study, the concept of field capacity was revisited and adapted to practical agronomic heuristics. By resorting to the assessment of root-zone water storage capacity (W), we envision field capacity as a functional hydraulic parameter derived from synthetic irrigation scheduling scenarios to minimize drought stress, drainage, and nitrate leachate below the root zone. A functional analysis was carried out on a 135-cm-thick layered soil profile beneath maize in eastern Nebraska. On-farm irrigation scheduling applications and agricultural practices were recorded for 20 years (2001–2020) at a daily time step. Hydrus-1D was calibrated and validated with direct measurements of the soil water retention curve and soil water content data, respectively, in each soil layer. A set of functional field capacity values was derived from 24 irrigation scheduling scenarios, and the optimal water storage capacity at field capacity (W FC ) was approximately 50 cm (corresponding to about 80% saturation in the soil profile). An average irrigation amount of 217.5 mm distributed over 21 events was obtained by using optimal irrigation scheduling, which was initiated when the matric pressure head took on a value of –700 cm and the irrigation rate was set at 1.0 cm d –1 . This irrigation practice ensured water storage at approximately the same level (ideally at W FC ) by sustaining only evapotranspiration fluxes in the uppermost portion of the root zone and by limiting excessive drainage. This protocol can be transferred to other agricultural fields.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Non-DNA radiosensitive targets that initiate persistent behavioral deficits in rats exposed to space radiation

Predicting future CNS risks for astronauts during deep-space missions will rely substantially on ground-based rodent data with space-relevant ions and behaviors. For rats, the accumulated evidence indicates that less densely ionizing radiation, such as 4 He and 12 C ions, induce behavior deficits at lower doses than densely ionizing ions, such as 48 Ti and 56 Fe. However, this observation conflicts with standard somatic radiobiology, in which densely ionizing ions are generally more effective than less densely ionizing ions, and where the DNA/nucleus is the accepted target for radiation-induced tumorigenesis, cytogenetic aberrations, genetic mutations, and reproductive cell death. To gain deeper insight into the subcellular nature of the radiation targets for behavior risks, we compared the effects of dose, fluence, and linear energy transfer (LET) of 4 He and 56 Fe particles using existing datasets for four distinct behavioral outcomes in rats: elevated plus maze (EPM-anxiety), novel object recognition (NOR-memory), operant responding (OR-response to environmental stimuli), and attentional set-shifting (ATSET-cognitive flexibility). We confirmed that less densely ionizing particles (except protons) showed ~100-fold lower threshold doses than densely ionizing particles for behavioral deficits (0.1–1 cGy for 4 He vs. 15–100 cGy for 56 Fe). However, when analyzed by fluence the behavioral responses converged, indicating that 4 He and 56 Fe were equally effective on a per-track basis. When analyzed by LET, there were ~100-fold differences in the LET for maximum effectiveness for behavioral deficits and DNA endpoints (~1 vs ~100 keV/μm, respectively). These unique features of radiation-induced behavioral deficits (high sensitivity to particles in the 1-keV/μm range, insensitivity to protons in the 0.2 keV/μm range, and isofluence dependence for particles with LET>1 keV/μm) provide evidence in support of a new hypothesis of sub-micron sized radiosensitive targets for behavioral effects consistent with the thickness of plasma membranes and/or small subcellular structures, smaller than a whole synapse. Like our behavior findings, mouse immature oocyte killing which is known to have a plasma membrane target was also better explained by fluence, rather than dose. In contrast, fluence analyses for DNA/nuclear endpoints in somatic cells (e.g., tumor induction, chromosome aberrations) showed opposite results, suggesting that behavior targets are not DNA. Our findings raise questions regarding the identity of subcellular targets and the multi-cellular functional unit for behavior risks, low-dose susceptibility, and generalizability from rat to other species and astronauts.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

NASA NTRS1995

Forced Convection and Sedimentation Past a Flat Plate

The steady laminar flow of a well-mixed suspension of monodisperse solid spheres, convected steadily past a horizontal flat plate and sedimenting under the action of gravity, is examined. It is shown that, in the limit as Re approaches infinity and epsilon approaches 0, where Re is the bulk Reynolds number and epsilon is the ratio of the particle radius a to the characteristic length scale L, the analysis for determining the particle concentration profile has several aspects in common with that of obtaining the temperature profile in forced-convection heat transfer from a wall to a fluid stream moving at high Reynolds and Prandtl numbers. Specifically, it is found that the particle concentration remains uniform throughout the O(Re(exp -1/2)) thick Blasius boundary layer except for two O(epsilon(exp 2/3)) thin regions on either side of the plate, where the concentration profile becomes non-uniform owing to the presence of shear-induced particle diffusion which balances the particle flux due to convection and sedimentation. The system of equations within this concentration boundary layer admits a similarity solution near the leading edge of the plate, according to which the particle concentration along the top surface of the plate increases from its value in the free stream by an amount proportional to X(exp 5/6), with X measuring the distance along the plate, and decreases in a similar fashion along the underside. But, unlike the case of gravity settling on an inclined plate in the absence of a bulk flow at infinity considered earlier, here the concentration profile remains continuous everywhere. For values of X beyond the region near the leading edge, the particle concentration profile is obtained through the numerical solution of the relevant equations. It is found that, as predicted from the similarity solution, there exists a value of X at which the particle concentration along the top side of the plate attains its maximum value phi(sub m) and that, beyond this point, a stagnant sediment layer will form that grows steadily in time. This critical value of X is computed as a function of phi(sub s), the particle volume fraction in the free stream. In contrast, but again in conformity with the similarity solution, for values of X sufficiently far removed from the leading edge along the underside of the plate, a particle-free region is predicted to form adjacent to the plate. This model, with minor modifications, can be used to describe particle migration in other shear flows, as, for example, in the case of crossflow microfiltration.

Pelekasis, Nikolaos A.↗

DOE OSTI2021

Enhanced orbital anisotropy through the proximity to a SrTiO 3 layer in the perovskite iridate superlattices

We have used angle-dependent soft x-ray absorption spectroscopy (XAS) at the O K edge and first-principles calculations to investigate the electronic structures of iridate-based superlattices ( SrIr O 3 ) m / ( SrTi O 3 ) ( m = 1 , 2, 3, and ∞). We focus on the pre-edge Ir 5 d t 2 g – O 2 p orbital hybridization feature in the XAS spectra. By varying the measurement geometry relative to the incident photon polarization, we are able to extract the dichroic contrast and observe the systematic increase in the anisotropy of Ir 5 d orbitals as m decreases. First-principles calculations elucidate the orbital anisotropy coming mainly from the enhanced out-of-plane compression of Ir O 6 octahedra in the SrIr O 3 layers that are adjacent to the inserted SrTi O 3 layers. As m decreases, the increased volume fraction of these interfacial SrIr O 3 layers and their contact with the SrTi O 3 layers within the ( SrIr O 3 ) m / ( SrTi O 3 ) supercell lead to enhanced orbital anisotropy. Furthermore, the tilt and rotation of Ir O 6 octahedra are shown to be essential to understand the subtle orbital anisotropy in these superlattices, and constraining these degrees of freedom will give an incorrect trend. Overall, our results demonstrate that the structural constraint from the inserted SrTi O 3 layers, in addition to other electronic means such as polar interface and charge transfer, can serve as a knob to control the orbital degree of freedom in these iridate-based superlattices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS2004

Improved Estimate of Phobos Secular Acceleration from MOLA Observations

We report on new observations of the orbital position of Phobos, and use them to obtain a new and improved estimate of the rate of secular acceleration in longitude due to tidal dissipation within Mars. Phobos is the inner-most natural satellite of Mars, and one of the few natural satellites in the solar system with orbital period shorter than the rotation period of its primary. As a result, any departure from a perfect elastic response by Mars in the tides raised on it by Phobos will cause a transfer of angular momentum from the orbit of Phobos to the spin of Mars. Since its discovery in 1877, Phobos has completed over 145,500 orbits, and has one of the best studied orbits in the solar system, with over 6000 earth-based astrometric observations, and over 300 spacecraft observations. As early as 1945, Sharpless noted that there is a secular acceleration in mean longitude, with rate (1.88 + 0.25) 10(exp -3) degrees per square year. In preparation for the 1989 Russian spacecraft mission to Phobos, considerable work was done compiling past observations, and refining the orbital model. All of the published estimates from that era are in good agreement. A typical solution (Jacobson et al., 1989) yields (1.249 + 0.018) 10(exp -3) degrees per square year. The MOLA instrument on MGS is a laser altimeter, and was designed to measure the topography of Mars. However, it has also been used to make observations of the position of Phobos. In 1998, a direct range measurement was made, which indicated that Phobos was slightly ahead of the predicted position. The MOLA detector views the surface of Mars in a narrow field of view, at 1064 nanometer wavelength, and can detect shadows cast by Phobos on the surface of Mars. We have found 15 such serendipitous shadow transit events over the interval from xx to xx, and all of them show Phobos to be ahead of schedule, and getting progressively farther ahead of the predicted position. In contrast, the cross-track positions are quite close to the predicted values. Assuming that the along-track discrepancy is small enough that we can linearize the corrections, we model the mean orbital longitude as a quadratic function of time, and solve for corrections to the constant, linear, and quadratic terms. The time span of the recent observations is insufficient to properly resolve this issue alone, but when the 127 years of prior observations are added, we find a solution which reduces misfit to the new observations considerably, and makes no significant change to the fit to earlier observations. Our estimate for the secular acceleration term is (1.367 + 0.006) degrees per square year. The corresponding rate of energy dissipation is 3.34 MW. From a geophysical perspective, a more interesting parameter than the secular acceleration itself is the tidal lag angle, or tidal quality factor Q, for Mars. Unfortunately, the limiting error source in that determination is remaining uncertainty in the tidal Love numbers at harmonic degrees 2,3, and even 4. Until those parameters are better constrained, improvement in the orbital model of Phobos will not provide corresponding benefits for understanding the interior of Mars.

Bills, Bruce↗

DOE OSTI2023

Budding yeasts in the subphylum Saccharomycotina Genome sequencing and assembly

Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial reads from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.

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DOE OSTI2023

Unifying principles for catalytic hydrotreating processes (Final Technical Report)

This project builds on the hypothesis that the hydrotreating processes for the removal of oxygen and sulfur are fundamentally similar at the atomic-scale and existing knowledge from the treatment of petroleum derived feedstock can be leveraged for the design of novel catalysts for the upgrade of bio-oil. We tested this hypothesis by comparing computed potential energy diagrams for hydrodesulfurization (HDS) of thiophene over MoS 2 with hydrodeoxygenation (HDO) of furan over MoO 3 and concluded that certain aspects, such as catalyst promotion with transition metals, are valid strategies for both reactions. On the other hand, we also noticed significant differences in the mechanism for hydrogen (H 2 ) activation, which requires sites with metallic character. While MoS 2 is known to have metallic edge states that can catalyze H 2 dissociation, this elementary step is prohibitively slow on defect-free oxides. Only in the presence of vacancies or by creating metal/oxide interfaces can efficient H 2 activation sites during HDO be formed. The need for bifunctional catalyst when it comes to efficient and selective HDO or dehydrogenation reactions was further corroborated in joint experimental and theoretical studies of the Guerbet reaction for the coupling of biomass derived oxygenates over PdCu alloys, nitrate reduction over In-promoted Pd nanoparticles, and ethylene dehydroaromatization over Ga-exchanged ZSM-5 zeolites. All of these catalytic systems have in common that catalytic sites with distinct functional requirements are needed to create a working catalyst. Detailed computational studies were carried out for HDO of m -cresol and phenol on Ru-modified TiO 2 surfaces, which allowed us to attribute catalytic activity to the metal/oxide interface. A surprising finding was that heterolytic cleavage of the H-H bond across the Ru/TiO 2 interface was critically important, despite lower barriers for homolytic H 2 activation on Ru metal. The explanation lies in the high barriers for hydrogen spillover from Ru to TiO 2 , which becomes unnecessary in the heterolytic activation pathway. Moreover, we also reported that proton transfer steps between metal and oxide sites are mediated by weakly adsorbed surface water. During attempts to develop and validate a kinetic Monte Carlo (kMC) model for HDO reactions at the Ru/TiO 2 interface, it became clear that lateral interactions are paramount to describe realistic surface chemistry and without these interactions, the reduction and hydroxylation behavior from our simulations was inconsistent with reported experiments. To assess the importance of lateral interactions in popular computational catalyst design strategies relying on the identification of reactivity descriptors, which can be used along with Brønsted–Evans–Polanyi (BEP) and scaling relations as input to a microkinetic model (MKM) to make predictions for activity or selectivity trends, we compared predicted trends with those obtained from descriptor-based kMC models. We critically evaluated the benefits of kMC over MKM in terms of trend predictions and computational cost when using only a small set of input parameters. After confirming that in the absence of lateral interactions the kMC and MKM approaches yield identical trends and mechanistic information, we observed substantial differences between the two kinetic models when lateral interactions were introduced. The mean-field implementation applies coverage corrections directly to the descriptors, causing an artificial overprediction of the activity of strongly binding metals. In contrast, the cluster expansion in kMC implementation can differentiate among the highly active metals but it is very sensitive to the set of included interaction parameters. Considering that computational screening relies on a minimal set of descriptors, for which MKM makes reasonable trend predictions at a ca. three orders of magnitude lower computational cost than kMC, we concluded that the MKM approach does provide an overall better entry point for computational catalyst design. Overall, this project has led to 11 peer-reviewed publications, and their scientific is impact is well illustrated by their combined 702 citations.

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