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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2023

KiT-RT: An Extendable Framework for Radiative Transfer and Therapy

Here, in this article, we present Kinetic Transport Solver for Radiation Therapy (KiT-RT), an open-source C++-based framework for solving kinetic equations in therapy applications available at https://github.com/CSMMLab/KiT-RT . This software framework aims to provide a collection of classical deterministic solvers for unstructured meshes that allow for easy extendability. Therefore, KiT-RT is a convenient base to test new numerical methods in various applications and compare them against conventional solvers. The implementation includes spherical harmonics, minimal entropy, neural minimal entropy, and discrete ordinates methods. Solution characteristics and efficiency are presented through several test cases ranging from radiation transport to electron radiation therapy. Due to the variety of included numerical methods and easy extendability, the presented open-source code is attractive for both developers, who want a basis to build their numerical solvers, and users or application engineers, who want to gain experimental insights without directly interfering with the codebase.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms

Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.

09 BIOMASS FUELS↗
DOE OSTI2024

Diverse signatures of convergent evolution in cactus-associated yeasts

Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning–based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall–degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle—and perhaps more generally lifestyles favoring thermotolerance—might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

Antifungal drug resistance is a major challenge in fungal infection management. Numerous genomic changes are known to contribute to acquired drug resistance in clinical isolates of specific pathogens, but whether they broadly explain natural resistance across entire lineages is unknown. We leveraged genomic, ecological, and phenotypic trait data from naturally sampled strains from nearly all known species in subphylum Saccharomycotina to examine the evolution of resistance to eight antifungal drugs. The phylogenetic distribution of drug resistance varied by drug; fluconazole resistance was widespread, while 5-fluorocytosine resistance was rare, except in Lipomycetales. A random forest algorithm trained on genomic data predicted drug-resistant yeasts with 54–75% accuracy. Fluconazole resistance was consistently predicted with the highest accuracy (75.2%). Furthermore, fluconazole resistance prediction accuracy was similar between models trained on genome-wide variation in the presence and number of InterPro protein annotations across Saccharomycotina (75.2%) and those trained on amino acid sequence alignment data of Erg11, a protein known to be involved in fluconazole resistance (74.3-74.9%). Interestingly, the top Erg11 residues for predicting fluconazole resistance across Saccharomycotina do not overlap with, are not spatially close to, and are less conserved than those previously linked to resistance in clinical isolates of Candida albicans. In silico deep mutational scanning of the C. albicans Erg11 protein reveals that amino acid variants implicated in clinical cases of resistance are almost universally destabilizing while variants in our most informative residues are energetically more neutral, explaining why the latter are much more common than the former in natural populations. Importantly, previous experimental analyses of C. albicans Erg11 have shown that amino acid variation in our most informative residues, despite having never been directly implicated in clinical cases, can directly contribute to resistance. Our results suggest that studies of natural resistance in yeast species never encountered in the clinic will yield a fuller understanding of antifungal drug resistance.

Harrison, Marie-Claire [Vanderbilt Univ., Nashvill↗
DOE OSTI2023

Dense Nuclear Matter Equation of State from Heavy-Ion Collisions

The nuclear equation of state (EOS) is at the center of numerous theoretical and experimental efforts in nuclear physics, motivated by its crucial role in our understanding of the properties of nuclear matter found on Earth, in neutron stars, and in neutron-star mergers. With advances in microscopic theories for nuclear interactions, the availability of experiments probing nuclear matter under conditions not reached before, and the advent of multi-messenger astronomy, the next decade will bring new opportunities for determining the nuclear matter EOS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

First Principles Molecular Dynamics Simulations of Ammonia Adsorption onto MFI Zeolite Nanosheets

MFI zeolite nanosheets membranes are promising candidates for ammonia separation from nitrogen and hydrogen, yet questions remain on the origin of their high selectivity. Silanols, Si-OH, are present in high concentration at the surface of zeolite nanosheets, and force-field-based simulations indicate that surface adsorption at the silanols contributes to selectivity. Silanols can chemically react with ammonia, which may further contribute to the ability of zeolite nanosheet membranes to separate it from other gases. In this work, we use first-principles molecular dynamics techniques to simulate ammonia’s behavior within stacked MFI zeolite nanosheets. We find that at 523 K and a loading corresponding to 35 bar, conditions desired for the ammonia separation, about 30% of ammonia reacts with surface silanols. Our work explores H-bonding and proton transfer within this system.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Mitochondrial genome diversity across the subphylum Saccharomycotina

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.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Further Investigation on Chromospheric and Prominence Activity of the RS Canum Venaticorum Star SZ Piscium

To continue our study on chromospheric activity and detection for possible prominence events of the very active RS Canum Venaticorum star SZ Piscium (SZ Psc), long-term high-resolution spectroscopic observations were obtained during several observing runs from 2014 to 2018. Based on the spectral subtraction technique, the chromospheric emission of the Ca ii IRT (λ8662, λ8542, and λ8498), H{sub α}, Na i D{sub 1}, D{sub 2} doublet, H{sub β}, and Ca ii H & K lines is mainly associated with the K1 IV primary star of the SZ Psc system, in good agreement with the previous studies, and the F8 V secondary star also shows some chromospheric emission, implying its active chromosphere. Moreover, an optical flare characterized by the He i D{sub 3} line emission together with stronger emission in the other indicators was detected. Furthermore, two chromospheric active longitudes around the two quadratures of the system were identified for most of the time, and the chromospheric activity shows significant changes during a few orbital cycles. The chromospheric activity level seems to show a long-term variation during our observations. There were some excess absorption features in the subtracted H{sub α} line and the other activity indicators, which would be caused by prominence-like materials associated with the K1 IV primary star of the system. Prominence materials could absorb the chromospheric emission and continuum from the K1 IV primary star and even the F8 V secondary one.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Atmospheric H 2 observations from the NOAA Cooperative Global Air Sampling Network

Abstract. The NOAA Global Monitoring Laboratory (GML) measures atmospheric hydrogen (H2) in grab samples collected weekly as flask pairs at over 50 sites in the Cooperative Global Air Sampling Network. Measurements representative of background air sampling show higher H2 in recent years at all latitudes. The marine boundary layer (MBL) global mean H2 was 552.8 ppb in 2021, 20.2 ± 0.2 ppb higher compared to 2010. A 10 ppb or more increase over the 2010–2021 average annual cycle was detected in 2016 for MBL zonal means in the tropics and in the Southern Hemisphere. Carbon monoxide measurements in the same-air samples suggest large biomass burning events in different regions likely contributed to the observed interannual variability at different latitudes. The NOAA H2 measurements from 2009 to 2021 are now based on the World Meteorological Organization Global Atmospheric Watch (WMO GAW) H2 mole fraction calibration scale, developed and maintained by the Max Planck Institute for Biogeochemistry (MPI-BGC), Jena, Germany. GML maintains eight H2 primary calibration standards to propagate the WMO scale. These are gravimetric hydrogen-in-air mixtures in electropolished stainless steel cylinders (Essex Industries, St. Louis, MO), which are stable for H2. These mixtures were calibrated at the MPI-BGC, the WMO Central Calibration Laboratory (CCL) for H2, in late 2020 and span the range 250–700 ppb. We have used the CCL assignments to propagate the WMO H2 calibration scale to NOAA air measurements performed using gas chromatography and helium pulse discharge detector instruments since 2009. To propagate the scale, NOAA uses a hierarchy of secondary and tertiary standards, which consist of high-pressure whole-air mixtures in aluminum cylinders, calibrated against the primary and secondary standards, respectively. Hydrogen at the parts per billion level has a tendency to increase in aluminum cylinders over time. We fit the calibration histories of these standards with zero-, first-, or second-order polynomial functions of time and use the time-dependent mole fraction assignments on the WMO scale to reprocess all tank air and flask air H2 measurement records. The robustness of the scale propagation over multiple years is evaluated with the regular analysis of target air cylinders and with long-term same-air measurement comparison efforts with WMO GAW partner laboratories. Long-term calibrated, globally distributed, and freely accessible measurements of H2 and other gases and isotopes continue to be essential to track and interpret regional and global changes in the atmosphere composition. The adoption of the WMO H2 calibration scale and subsequent reprocessing of NOAA atmospheric data constitute a significant improvement in the NOAA H2 measurement records.

Pétron, Gabrielle↗
DOE OSTI2022

Genetically modified cells that produce C6-C10 fatty acid derivatives

Genes encoding mutant 3-ketoacyl-CoA synthases are introduced into host cells. Certain of the mutants enhance the production of shorter-chain fatty acids and derivatives by the cell than do the wild-type (unmutated) enzymes. In other cases, the chain length is not significantly affected, but productivity is enhanced. In specific cases, both a shift toward lower chain length and higher productivity is seen. Cells producing the mutant 3-ketoacyl-CoA synthases are especially suitable for producing C6-C10 fatty acids and derivatives.

Liao, Hans H.↗