Search NASA⌕ Search

SEARCH · Search NASA

Results for “Substitutional species”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Mapping Support for Targeted Critical Minerals Exploration and Extraction

The United States’ dependency on imported minerals poses significant risks to economic stability and national security due to potential supply disruptions. Recognizing the strategic importance of critical minerals, the Department of Energy (DOE) emphasizes the need for a secure and resilient supply chain to support emissions reduction, technology development, and capitalization on clean energy opportunities. The DOE’s Office of Manufacturing and Energy Supply Chains (MESC), in collaboration with the Office of Policy (OP), addresses these vulnerabilities by focusing on upstream domestic critical minerals production, balancing extraction with social and environmental goals, including conservation, environmental justice, and respect for Tribal sovereignty. This report showcases a collaborative effort involving Idaho National Laboratory (INL), Argonne National Laboratory (Argonne), National Renewable Energy Laboratory (NREL), and the U.S. Geological Survey (USGS) to map mineral development potential along with key social and environmental datasets. A geographical information system (GIS)-based web map application was developed as a preliminary tool for environmental analysis, integrating 158 geospatial data layers such as critical habitat, land ownership, economic indicators, and environmental concerns. Data were sourced from agencies like the Bureau of Land Management (BLM) and USGS and processed using GIS technology to enhance visualization and analysis. The proposed analysis framework categorizes areas into high, mid, and low concern based on withdrawn lands, special status species, the Economic Development Capacity Index (EDCI) Mining Composite Index, and the Climate and Economic Justice Screening Tool (CEJST). While the application provides broad visualizations, it is not a substitute for detailed environmental reviews required under the National Environmental Policy Act (NEPA). Users must conduct further analyses and engage with tribal entities and other stakeholders for comprehensive planning. A case study of the Idaho Cobalt Belt (ICB) in Lemhi County, Idaho, has been provided in the report to illustrate the tool's practical use. This report introduces a GIS application and framework to support stakeholders in identifying and prioritizing areas for critical mineral exploration, promoting secure supply chains, and advancing the nation's energy independence through responsible resource stewardship.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The evolution of anaerobic growth in Saccharomycotina yeasts

Humans rely on the ability of budding yeasts to grow without oxygen in industrial scale fermentations that produce beverages, foods, and biofuels. Oxygen is deeply woven into the energy metabolism and biosynthetic capabilities of budding yeasts. While diverse ecological habitats may provide wide varieties of different carbon and nitrogen sources for yeasts to utilize, there is no direct substitute for molecular oxygen, only a range of availability. Understanding how a small subset of budding yeasts evolved the ability to grow without oxygen could expand the set of useful species in industrial scale fermentations as well as provide insight into the cryptic field of yeast ecology. Furthermore, we still do not yet appreciate the full breadth of species that can growth without oxygen, what genes underlie this adaptation, and how these genes have evolved.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Holistic design principles for flow batteries: Cation dependent membrane resistance and active species solubility

Cation dependent resistance of a commercial cation exchange membrane, Nafion™ 212, as well as the solubility of select active materials are investigated, demonstrating practical consequences of cation choice on redox flow battery (RFB) performance. The conductivity of alkali and methyl- or -alcohol substituted ammonium cations through pretreated Nafion™ 212 reveal that cation size is the dominant factor affecting ionic transport. Among the alkali series the resistance increases with larger ionic radii and similarly, with increasing steric bulk through substitution on ammonia. The solubility of ferrocyanide, a commonly used redox flow battery posolyte (or catholyte), as well as iron, cobalt, and chromium metal-organic compounds are determined for the same series of cations. Full cells are assembled using various cation mixtures and membrane pre-treatments to demonstrate practical effects of each variable. Here, we highlight the need to carefully select the correct cations for efficient electrolyte design, since certain cations may lead to high conductivity but low solubility, or vice versa, and provide design principles for RFBs using Nafion™ 212.

25 ENERGY STORAGE↗
DOE OSTI2022

Photoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate addition

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical con- jugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Here, mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

fpikachu96/KRED-data

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical conjugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

Huang, Xiaoqiang↗
DOE OSTI2020

Stable and Catalytically Active Shape-Engineered Cerium Oxide Nanorods by Controlled Doping of Aluminum Cations

Shape-engineered nanocrystals (SENs) promise a better selectivity and a higher activity in catalytic reactions than the corresponding non-shape-engineered ones because of their larger specific surface areas and desirable crystal facets. However, often, it is challenging to apply SENs in practical catalytic applications at high reaction temperatures, where SENs deforms into more stable, less active nanoparticles. In this paper, we show that atomic layer deposition (ALD) of Al 2 O 3 at 200 °C can controllably dope Al cations into the shape-engineered CeO 2 nanorods (NRs) to not only increase their shape transition temperature from 400 °C to beyond 700 °C but also greatly increase their specific reversible oxygen storage capacity (srOSC). Furthermore, the substituted Al3+ ions impede the surface diffusion of Ce ions and therefore improve the thermal stability of CeO 2 NRs. These Al3+ dopants form -Al–O–Ce–O– clusters, which are new Ce species and can be reversibly reduced and oxidized at 500–700 °C. This low-temperature chemical doping method decouples the synthesis process of SENs from the doping process and maintains the shape of the SENs during the activation of dopants. This concept could be adopted to enable the applications of other SENs in challenging high-temperature environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Isotopic Substitution Reveals the Importance of Aluminate Diffusion Dynamics in Gibbsite (Al(OH) 3 ) Crystallization from Alkaline Aqueous Solution

Understanding molecular-scale factors governing the precipitation of aluminum hydroxides, such as gibbsite, under alkaline conditions is important for the formation of laterite deposits, as well as aluminum processing. However, mechanisms enabling tetrahedral aluminate ions to assemble into octahedral sites of the gibbsite lattice remain unclear. Formation of oligomeric complexes has been hypothesized as a critical intermediate step. Here, we report a study of gibbsite solubility in highly alkaline solutions using deuterium substitution to probe equilibrium and kinetic factors that could affect oligomeric intermediate formation, including the reactivity and the diffusivity of aluminate ions. When substituting sodium hydroxide with sodium deuteroxide, solution analysis shows a nearly 40% and 50% increase in gibbsite solubility in 2.4 and 3.3 mol·kg –1 total sodium solutions, respectively. Raman spectroscopy indicated that monomeric aluminate ions are the predominant species in solution irrespective of deuteration. However, both 27 Al and 23 Na nuclear magnetic resonance (NMR) spectroscopy revealed significant differences in chemical shifts in deuterated solutions, and analysis of 1 H, 23 Na, and 27 Al diffusion coefficients with pulsed-field gradient, stimulated echo NMR spectroscopy shows a decrease in ion diffusivity with increasing total deuterium in solution, consistent with the notion of increasing strength in the hydrogen/deuterium bonding network. In conclusion, because the relative change in 1 H diffusion coefficients are commensurate with the difference in apparent solubility constants, there is evidence for an oligomeric intermediate whose steady-state concentration is maintained by the collision frequency of aluminate ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

CRISPR-prime editing, a versatile genetic tool to create specific mutations with a single nucleotide resolution in Leptospira

ABSTRACT Leptospirosis, caused by pathogenic bacteria from the genusLeptospira, is a global zoonosis responsible for more than one million human cases and 60,000 deaths annually. The disease also affects many domestic animal species. Historically, genetic manipulation ofLeptospirahas been difficult to perform, resulting in limited knowledge on pathogenic mechanisms of disease and the identification of virulence factors. The application of CRISPR/Cas9 and its variations have helped fill these gaps but the generation of knockout mutants remains challenging because double-strand breaks (DSBs) inflicted by Cas9 nuclease are lethal toLeptospiracells. The novel CRISPR prime editing (PE) strategy is the first precise genome-editing technology that allows deletions, insertions, and base substitutions without introducing DSBs. This revolutionary technique utilizes a nickase Cas9 that cleaves a single strand of DNA, coupled with an engineered reverse transcriptase and a modified single-guide RNA (termed prime editing guide RNA) containing an extended 3′ end with the desired edits. We demonstrate the application of CRISPR-PE in both saprophytic and pathogenicLeptospirafrom multiple species and serovars by introducing deletions or insertions into target DNA with a remarkable precision of just one nucleotide. Additionally, we demonstrate the ability to genetically manipulateLeptospira borgpetersenii, a prevalent pathogenic species of humans, domestic cattle, and wildlife animals. Rapid plasmid loss by mutated strains in liquid culture allows for the generation of knockout strains without selective markers, which can be readily used to elucidate virulence factors and develop optimized bacterin and/or live vaccines against leptospirosis. IMPORTANCE Leptospirosis is a geographically widespread bacterial zoonosis. Genetic manipulation of pathogenicLeptospiraspp. has been laborious and difficult to perform, limiting our ability to understand how leptospires cause disease. The application of the CRISPR/Cas9 system toLeptospiraenhanced our ability to generate knockdown and knockout mutants; however, the latter remains challenging. Here, we demonstrate the application of the CRISPR prime editing technique inLeptospira, allowing the generation of knockout mutants in several pathogenic species, with mutations comprising just a single nucleotide resolution. Notably, we generated a mutant in theLeptospira borgpeterseniibackground, a prevalent pathogenic species of humans and cattle. Our application of this method opens new avenues for studying pathogenic mechanisms ofLeptospiraand the identification of virulence factors across multiple species. These methods can also be used to facilitate the generation of marker-less knockout strains for updated and improved bacterin and/or live vaccines.

Microbiology↗
DOE OSTI2020

Near Neutral pH Redox Flow Battery with Low Permeability and Long-Lifetime Phosphonated Viologen Active Species

A highly stable phosphonate-functionalized viologen is introduced in this work as the redox-active material in a negative potential electrolyte for aqueous redox flow batteries (ARFBs) operating at nearly neutral pH. The solubility is 1.23 m and the reduction potential is the lowest of any substituted viologen utilized in a flow battery, reaching –0.462 V versus SHE at pH = 9. The negative charges in both the oxidized and the reduced states of 1,1'-bis(3-phosphonopropyl)-[4,4'-bipyridine]-1,1'-diium dibromide ( BPP–Vi ) effect low permeability in cation exchange membranes and suppress a bimolecular mechanism of viologen decomposition. A flow battery pairing BPP–Vi with a ferrocyanide-based positive potential electrolyte across an inexpensive, non-fluorinated cation exchange membrane at pH = 9 exhibits an open-circuit voltage of 0.9 V and a capacity fade rate of 0.016% per day or 0.00069% per cycle. Overcharging leads to viologen decomposition, causing irreversible capacity fade. Our research introduces extremely stable, extremely low-permeating and low reduction potential redox active materials into near neutral ARFBs.

25 ENERGY STORAGE↗
DOE OSTI2021

Magnetic ground state of the one-dimensional ferromagnetic chain compounds M (NCS) 2 (thiourea) 2 (M=Ni,Co)

The magnetic properties of the two isostructural molecule-based magnets— Ni ( NCS ) 2 ( thiourea ) 2 , S = 1 [ thiourea = SC ( NH 2 ) 2 ] and Co ( NCS ) 2 ( thiourea ) 2 , S = 3 / 2 —are characterized using several techniques in order to rationalize their relationship with structural parameters and to ascertain magnetic changes caused by substitution of the spin. Zero-field heat capacity and muon-spin relaxation measurements reveal low-temperature long-range ordering in both compounds, in addition to Ising-like ( D < 0 ) single-ion anisotropy ( D Co ~ - 100 K, D Ni ~ - 10 K). Crystal and electronic structure, combined with dc-field magnetometry, affirm highly quasi-one-dimensional behavior, with ferromagnetic intrachain exchange interactions J Co ≈ + 4 K and J Ni ~ + 100 K and weak antiferromagnetic interchain exchange, on the order of J ' ~ - 0.1 K. Furthermore, electron charge- and spin-density mapping reveals through-space exchange as a mechanism to explain the large discrepancy in J -values despite, from a structural perspective, the highly similar exchange pathways in both materials. Both species can be compared to the similar compounds M Cl 2 ( thiourea ) 4 , M = Ni(II) (DTN) and Co(II) (DTC), where DTN is known to harbor two magnetic-field-induced quantum critical points. Direct comparison of DTN and DTC with the compounds studied here shows that substituting the halide Cl - ion for the NCS - ion results in a dramatic change in both the structural and magnetic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Cross-species analysis of FcγRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque

Introduction Antibodies play a critical role in immunity in part by mediating clearance of pathogens and infected cells by antibody-dependent cellular phagocytosis (ADCP) through engagement of Fc gamma receptors (FcγRs) on innate immune cells. Among these, FcγRIIa (CD32a) is a key activating receptor expressed on macrophages, dendritic cells, and other antigen-presenting cells. Its affinity for IgG and ability to mediate ADCP is influenced by allelic polymorphisms. In humans, a single amino acid polymorphism at position 131, where histidine (H) is substituted with arginine (R), leads to decreased IgG1 and IgG2 subclass binding affinity and, consequently, lower efficiency of phagocytic responses. Rhesus macaques ( Macaca mulatta ), which are widely used as nonhuman primate models, exhibit a similar polymorphism at position 131 of FcγRIIa, but with arginine replaced by proline (P). Here, we investigated structure-function relationships associated with the FcγRIIa polymorphism at position 131 in both species, specifically with respect to IgG1 and IgG2. Methods We determined the structures of complexes formed by each variant with IgG1 Fc and those formed by the higher affinity variant with IgG2 Fc for both species by x-ray crystallography and linked these structures to affinity and activity using SPR and an ADCP assay. We also determined the structure of human inhibitory FcγRIIb (CD32b) in complex with IgG1 Fc by x-ray crystallography. Results Through analysis of these structures, our studies reveal that FcγRIIa engagement is minimally influenced by Fc glycan composition, distinguishing it from FcγRIIIa whose affinity is strongly influenced by glycan-composition. Comparative structures of human and macaque FcγRIIa variants demonstrate species- and allele-specific differences in Fc binding, but our functional assays showed only minimal allele-specific effects in humans. In contrast, allele-specific effects in macaques were highly significant; the macaque P 131 variant showing uniformly reduced IgG affinity. Conclusion These insights highlight fundamental interspecies and allelic distinctions that are critical for interpreting FcγRIIa-mediated effector functions in macaque models and for optimizing translational antibody and vaccine design.

Tolbert, William D.↗
DOE OSTI2024

New proxies for second-order cumulants of conserved charges in heavy-ion collisions within the EPOS4 framework

Proxies for cumulants of baryon number 𝐵, electric charge 𝑄, and strangeness 𝑆 are usually measured in heavy-ion collisions via moments of net-number distribution of given hadronic species. Since these cumulants of conserved charges are expected to be sensitive to the existence of a critical point in the phase diagram of nuclear matter, it is crucial to ensure that the proxies used as substitutes are as close to them as possible. Hence, we use the EPOS 4 framework to generate Au + Au collisions at several collision energies of the BNL Relativistic Heavy Ion Collider beam energy scan. We compute second-order net cumulants of 𝜋, 𝐾, and 𝑝, for which experimental data have been published as well as the corresponding conserved charge cumulants. We then compare them with proxies, defined in previous lattice QCD and hadron resonance gas model studies, which are shown to reproduce more accurately their associated conserved charge cumulants. We investigate the impact of hadronic rescatterings occurring in the late evolution of the system on these quantities, as well as the amount of signal actually originating from the bulk medium which endures a phase transition.

Physics↗
DOE OSTI2024

Understanding the Electronic and Structural Effects in ORR Intermediate Binding on Anion‐Substituted Zirconia Surfaces

Abstract For oxygen reduction reaction (ORR), the surface adsorption energies of O and OH* intermediates are key descriptors for catalytic activity. In this work, we investigate anion‐substituted zirconia catalyst surfaces and determine that adsorption energies of O and OH* intermediates is governed by both structural and electronic effects. When the adsorption energies are not influenced by the structural effects of the catalyst surface, they exhibit a linear correlation with integrated crystal orbital Hamiltonian population (ICOHP) of the adsorbate‐surface bond. The influence of structural effects, due to the re‐optimisation slab geometry after adsorption of intermediate species, leads to stronger adsorption of intermediates. Our calculations show that there is a change in the bond order to accommodate the incoming adsorbate species which leads to stronger adsorption when both structural and electronic effects influence the adsorption phenomena. The insights into the catalyst‐adsorbate interactions can guide the design of future ORR catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Characterizing W sources in the all-W wall, all-RF WEST tokamak environment

In this work, experimental data, together with interpretive modeling tools, are examined to study trends in the tungsten (W) source in the all-W environment of the WEST tokamak, both from the divertor and from the main chamber. In particular, a poloidal limiter protecting an ion cyclotron resonance heating (ICRH) antenna is used as proxy for main chamber sourcing. The key study is carried out by stepping up lower hybrid current drive (LHCD) power, as the only auxiliary power source. Limiter and divertor W sources exhibit a qualitatively similar proportionality to the total power crossing the separatrix, P SEP , although the main chamber source remains substantially lower than the divertor source, for the range of P SEP accessible in the experiments. Intepretive modeling of the limiter source is carried out with a particle-in-cell (PIC) sheath model coupled to a surface sputtering model. Oxygen is used as a proxy for all light impurity species allowing for characterization of the critical W erosion regions. To get a good quantitative match to the data, it is necessary to assume that the oxygen arrives at the surface mostly at high ionization stages (4+ and above). A separate simulation with SOLEDGE-EIRENE, constrained to measured upstream scrape-off-layer plasma profiles, gives oxygen fractional abundances that are compatible with the PIC simulation result. This is understood to arise from transport processes that dominate over recombination. Substituting the LHCD by ICRH, in an equivalent experiment, the local W source exhibits a 3× enhancement. This can be matched by the simulation, by assuming local RF electric field rectification, based on ~100 eV peak-to-peak, near-antennna electric field. This work has highlighted the particular importance of understanding the ion charge state balance of light impurities as these are most likely the dominant sputtering species in fusion devices with high-Z walls.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Evaluating the Importance of Conformers for Understanding the Vacuum-Ultraviolet Spectra of Oxiranes: Experiment and Theory

Vacuum-ultraviolet (VUV) absorption spectroscopy enables electronic transitions that offer the unambiguous identification of molecules. As target molecules become more complex, multifunctional species present a great challenge to both experimental and computational spectroscopy. This research reports both experimental and theoretical studies of oxiranes. Computationally, the nuclear ensemble approach has been used to accurately predict experimental spectra for a variety of molecules. However, this approach incurs great computational cost, as ensembles generally consist of thousands of geometries. The present study aims to drastically reduce the ensemble by evaluating the significance of the conformers to the predicted spectra. This approach was applied to 11 substituted oxiranes using the Conformer Rotamer Ensemble Sampling Tool (CREST) of Grimme to generate an ensemble of unique conformers determined by their Boltzmann populations. Five TD-DFT functionals (BMK, CAM-B3LYP, M06-2X, MN15, ωB97X-D) and EOM-CCSD were used to simulate the spectrum of each substituted oxirane ensemble. Computed spectra were then compared to the experiment using both qualitative and quantitative metrics. Based on these metrics, it was observed that certain conformers may not be necessary to characterize this set of oxiranes despite the temperature (323 K) of the experiment. A single conformer can then be used with TD-DFT and EOM-CCSD to replicate the experimental spectra of these medium-sized combustion species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Immobilizing Pertechnetate in Ettringite via Sulfate Substitution

Until recently, a nuclear waste form did not exist for the immobilization and long-term storage of the anionic form of radionuclide technetium-99 (99Tc), pertechnetate (TcO 4 - ). Across international nuclear waste sites, the inability to capture TcO 4 - poses a threat to the local environment due to the anion’s long half-life and environmental mobility under environmentally oxic conditions. To combat this challenge, most waste forms would capture 99Tc using materials that reduce TcO 4 - to Tc(IV) species, e.g. 99Tc oxides or 99Tc sulfides. However, this is a short-lived solution unless reducing capacities can be regenerated to last over the long life expectancy of some nuclear waste forms (~10,000 years). In light of recent experimental observations gained from the development of cementitious waste forms and unconfirmed hypotheses from the literature, this work explores how ettringite, a common mineral formed in cementitious materials with demonstrated success in incorporating oxyanions, may be used to immobilize TcO 4 - directly and over the life-time of the waste form. Using batch precipitation experiments, solid phase characterization techniques, and ab initio molecular dynamics simulations, we demonstrate herein successful incorporation of TcO 4 - into ettringite via substitution for SO 4 2- within the ettringite crystal structure. Here, these results are first of their kind and confirm the hypothesis that ettringite acts as an immobilizing mineral within cementitious waste forms for the highly mobile TcO 4 - oxyanion, enhancing the overall performance of these waste forms over time.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis

Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We observe a high rate of fixation of non-synonymous substitutions in the Cbp1 coding sequences, indicating that Cbp1 is under positive selection. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel “binocular” fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a fungal virulence factor under positive selection that localizes to the cytosol to trigger host cell lysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Atom Identification in Bilayer Moiré Materials with Gomb-Net

Moiré patterns in van der Waals bilayer materials complicate the analysis of atomic-resolution images, hindering the atomic-scale insight typically attainable with scanning transmission electron microscopy. Here, we report a method to detect the positions and identities of atoms in each of the individual layers that compose twisted bilayer heterostructures. We developed a deep learning model, Gomb-Net, which identifies the coordinates and atomic species in each layer, deconvoluting the moiré pattern. This enables layer-specific mapping of atomic positions and dopant distributions, unlike other commonly used segmentation models which struggle with moiré-induced complexity. Using this approach, we explored the Se atom substitutional site distribution in a twisted fractional Janus WS 2 -WS 2(1–x) Se 2x heterostructure and found that layer-specific implantation sites are unaffected by the moiré pattern’s local energetic or electronic modulation. In conclusion, this advancement enables atom identification within material regimes where it was not possible before, opening new insights into previously inaccessible material physics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗