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One-Carbon Metabolism and SANS 2022 Update

Spaceflight Associated Neuro-ocular Syndrome, or SANS, affects a subset of astronauts (1, 2), and biochemical evidence has documented differences in those astronauts (3). Specifically, they had higher circulating concentrations of metabolites of the one-carbon metabolic pathway (1C), including homocysteine, and these concentrations were higher before flight (3). After ruling out many potential confounding factors in these otherwise healthy individuals (e.g., sex, kidney function, vitamin status, coffee consumption), a study of genetics was warranted. In an initial pilot effort, we documented a genetic predisposition to develop ophthalmic changes after long-duration space flight (4). That is, from a limited study of 5 single-nucleotide polymorphisms (SNPs), we found that the G allele for the MTRR A66G SNP was associated with a greater risk of choroidal folds and cotton-wool spots after flight, and the C allele for SHMT1 C1420T was protective against optic disc edema (4). These data provide a potential pathway for understanding why some individuals develop SANS, while others do not. The initial pilot study of 5 SNPs yielded striking findings, but the 1C pathway is far more complex. An effort was undertaken to examine more than 500 1C SNPs to see if a broader examination could help illuminate this association. That work is ongoing. The astronaut findings led us to advocate for the inclusion of 1C pathway genetic and biochemistry testing on other SANS-related projects, noting that genetics might help identify responders, non-responders, or outliers. The first such effort yielded evidence of an association of specific forms of the MTRR and SHMT-1 SNPs and vitamin B12 status with end-tidal CO2 after acute carbon dioxide exposure (5). The second such effort led to the identification that individuals exposed to strict head-down tilt and CO2 for 30-d who developed optic disc edema also had risk alleles for the two SNPs described above (6). Additionally, we identified a clinical population with many characteristics either attributed or purported to be involved in the ocular changes seen in affected astronauts: women with polycystic ovary syndrome (PCOS). PCOS is a condition of androgen excess and anovulatory menstrual cycles. The shared characteristics and clinical findings between SANS and PCOS generally include higher circulating homocysteine concentrations, increased retinal nerve fiber layer thickness, increased androgen concentrations (or responses), and altered carbohydrate metabolism. To our knowledge, no study has examined whether women with PCOS have asymptomatic ophthalmic anomalies observed in astronauts with SANS. While researchers have evaluated the one-carbon metabolism pathway polymorphisms of PCOS patients, and initial studies show an association with certain one-carbon polymorphisms, none have looked at the set of SNPs identified in our studies that are associated with ophthalmic changes in astronauts. Accordingly, we designed a study to evaluate the association of one-carbon pathway SNPs and ophthalmic findings in patients with PCOS and/or IIH compared to controls. Subjects provided blood samples for vitamin and one carbon biochemistry analyses, an extensive analysis of >500 SNPs associated with one carbon metabolism and had eye examinations and ocular imaging. Data analysis are underway. The data collected to date have shown associations between one carbon pathway biochemistry and genetics and incidence of SANS. The mechanisms for SANS has yet to be identified, although many hypotheses exist. Based on our data, we have developed (8, 9) and expanded (6) a multi-hit hypothesis for how these seemingly disparate findings could be linked. While intriguing, the hypothesis represents the starting point for further research. We aim to clarify the relationship between B-vitamin status and genetics with regard to the risk of SANS. Ultimately, understanding the mechanism(s) behind this will provide a means to predict, prevent, or treat these ophthalmologic pathologies in astronauts, and terrestrial populations.

S M Smith↗
DOE OSTI2023

Search for High-Pressure Silicon Phases: Reaching the Extreme Conditions with High-Intensity Laser Irradiation

Controlling electronic and optical properties of semiconducting materials could substantially expand their functionality and enable new pathways for the formation of ‘smart’ materials for emerging innovative applications. An emerging new path for the synthesis of exotic silicon (Si) polymorphs is irradiation of bulk diamond-cubic Si by ultrashort laser pulses at relativistic intensity above 1019 W/cm2. Exotic polymorphs are formed due to interaction with MeV-energy electrons generated in laser-produced high-temperature plasma state. The unusual Si structures are found in the form of 5–10 nm nanoparticles confined deep in the bulk of 500-μm-thick Si samples. Raman spectroscopy, electron microscopy and X-ray diffraction studies provide an unequivocal evidence of exotic Si phase formation. A key advantage of such relativistic irradiation lies thereby in the fact that large quantities of such exotic Si is synthesised embedded within the bulk diamond-cubic Si and that further the formed Si polymorphs are stable at ambient temperature and pressure. They are thus available for further studies for electronic applications in selective band gap engineering.

Rapp, Ludovic↗
DOE OSTI2020

Assessing Single-Source Reproducibility of Human Head Hair Peptide Profiling from Different Regions of the Scalp

Neither microscopical hair comparisons nor mitochondrial DNA sequencing alone, or together, constitutes a basis for personal identification. Due to these limitations, a complementary technique to compare questioned and known hair shafts was investigated. Recently, scientists from Lawrence Livermore National Laboratory's Forensic Science Center and other collaborators developed a peptide profiling technique, which can infer non-synonymous single nucleotide polymorphisms (SNPs) preserved in hair shaft proteins as single amino acid polymorphisms (SAPs). In this study, peptide profiling was evaluated to determine if it can meet forensic expectations when samples are in limited quantities with the possibility that hair samples collected from different areas of a single donor’s scalp (i.e., single source) might not exhibit the same SAP profile. The average dissimilarity, percent differences in SAP profiles within each source, ranged from 0% difference to 29%. This pilot study suggests that more work is needed before peptide profiling of hair can be considered for forensic comparisons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Topological effects on separation of alkane isomers in metal–organic frameworks

Polymorphism in metal–organic frameworks (MOFs) means that the same chemical building blocks (nodes and linkers) can be used to construct isomeric MOFs with different topological networks. The choice of topology can substantially impact the pore network of the MOF, changing the sizes and shapes of the pores, which has implications for adsorption and separation applications. Here, we look at the influence of topology in 38 polymorphic MOFs on the separation of linear and branched C4–C6 alkane isomers, a separation of great importance to the petrochemical industry. We find that the MOF Cu 2 (1,4-benzenedicarboxylate) in nbo topology (nbo-Cu 2 BDC) has particularly high affinity for linear alkanes due to its small pore size, which excludes the branched isomers. Upon studying this MOF in further detail, we find that it can take either of two conformations: a cubic conformation, which is typical of nbo MOFs, and a unique star conformation that contains 1D triangular and hexagonal channels. The determination of which conformation the MOF will adopt depends on steric effects between the nodes and linkers.

42 ENGINEERING↗
DOE OSTI2022

High temperature stability and transport characteristics of hydrogen in alumina via multiscale computation

Here, the impact of hydrogen charge states on the stability and transport characteristics of hydrogen interstitials in alumina polymorphs is evaluated by multiscale computational methods including density functional theory (DFT), ab initio molecular dynamics (AIMD) and machine learned force fields. Thermodynamic calculations show that the protonic H i +1 interstitial is the most stable defect species for most values of the electronic bandgap in both and amorphous alumina (Al 2 O 3 ). Further, active learned Gaussian approximation potentials (GAP) were developed using AIMD data to study temperature dependent long time proton diffusion in alumina. Diffusivity calculations from GAP-MD simulations are found to be comparable with of the AIMD data, while being ~340 times faster and scalable to larger systems. Comparisons with diffusivity values for other interstitial charge states (H i 0 and H i -1 ) and published experimental literature indicate that H i +1 diffusion is the likely mechanism of hydrogen transport. A good agreement is obtained between H i +1 diffusivity calculated in α-Al 2 O 3 from DFT: 5.05 10 -3 exp(-0.81 eV/k B /T) cm 2 /s and reported experiment: 9.7X10 -4 exp(-0.83 eV/k B /T) cm 2 /s. Computationally and experimentally calculated energy barriers (0.81 and 0.83 eV respectively) only differ by 2.5%. Similarly, the pre-exponential diffusion coefficients only differ by 0.5 orders of magnitude. Moreover, the diffusivity of H i +1 in amorphous Al 2 O 3 in the 1000–2000 K range is calculated to be 2.53X10 -2 exp(-0.89 eV/k B /T), just one order of magnitude higher than the corresponding value in α-Al 2 O 3 . This suggests that local structural disorder does not significantly affect the energy landscape and diffusion behavior of H i +1 in Al 2 O 3 . Overall, these results show promise for the application of alumina polymorphs as hydrogen permeation barriers.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Wafer-scale growth of two-dimensional, phase-pure InSe

Two-dimensional (2D) indium monoselenide (InSe) has attracted significant attention as an ultrathin III–VI semiconductor with a combination of favorable attributes that are comparable to those of III–V semiconductors and van der Waals 2D transition-metal dichalcogenides. Nevertheless, there has been no demonstration of large-area synthesis of 2D InSe due to the complexity of the binary In-Se system and the difficulties in promoting lateral growth. Here, we report the polymorph-selective synthesis of epitaxial 2D InSe by metal-organic chemical vapor deposition (MOCVD) over 2-in wafers. We achieve polymorph-selective epitaxial growth of InSe on c-plane sapphire via flow modulation to control the Se/In ratio. The layer-by-layer growth allows thickness control with tunable optical properties comparable to those of bulk crystals. We also demonstrate gate-tunable electrical transport with a field-effect mobility comparable to that of single-crystalline flakes. Importantly, these results indicate that InSe grown by MOCVD could be an effective channel material for back-end-of-line integration in logic transistors.

2D materials↗
DOE OSTI2022

Stabilized Synthesis of 2D Verbeekite: Monoclinic PdSe 2 Crystals with High Mobility and In-Plane Optical and Electrical Anisotropy

PdSe 2 has a layered structure with an unusual, puckered Cairo pentagonal tiling. Its atomic bond configuration features planar 4-fold-coordinated Pd atoms and intralayer Se–Se bonds that enable polymorphic phases with distinct electronic and quantum properties, especially when atomically thin. PdSe 2 is conventionally orthorhombic, and direct synthesis of its metastable polymorphic phases is still a challenge. Here, we report an ambient-pressure chemical vapor deposition approach to synthesize metastable monoclinic PdSe 2 . Monoclinic PdSe 2 is shown to be synthesized selectively under Se-deficient conditions that induce Se vacancies. These defects are shown by first-principles density functional theory calculations to reduce the free energy of the metastable monoclinic phase, thereby stabilizing it during synthesis. Further, the structure and composition of the monoclinic PdSe 2 crystals are identified and characterized by scanning transmission electron microscopy imaging, convergent beam electron diffraction, and electron energy loss spectroscopy. Polarized Raman spectroscopy of the monoclinic PdSe 2 flakes reveals their strong in-plane optical anisotropy. Electrical transport measurements show that the monoclinic PdSe 2 exhibits n-type charge carrier conduction with electron mobilities up to ~298 cm 2 V –1 s –1 and a strong in-plane electron mobility anisotropy of ~1.9. The defect-mediated growth pathway identified in this work is promising for phase-selective direct synthesis of other 2D transition metal dichalcogenides.

2D material↗
DOE OSTI2022

Unexpected features in the optical vibrational spectra of δ-UO 3

Uranium trioxide displays a complex chemical phase space, with at least six structurally distinct polymorphs accessible via different synthetic routes. Remarkably, despite its technological importance, full structural and electronic characterization of these polymorphs remains an open area of study. δ-UO 3 in particular has attracted significant theoretical attention due to its high point group and space group symmetries, having U (VI) in octahedral coordination with polyhedra interconnected through corner-sharing to build a 3-D cubic lattice with space group symmetry Pm-3m and Z = 1. Critical experimental information, such as its optical vibrational spectra, are not known. Here, we study the Raman and infrared (IR) spectra of δ-UO 3 together with the support of density functional theory (DFT) calculations for spectral interpretation. A symmetry analysis of the DFT-predicted phonon eigenmodes indicates that δ-UO 3 should have two IR active modes and no Raman active modes. Experimental results, however, indicate significant Raman scattering from δ-UO 3 . We therefore propose four potential explanations for this apparent contradiction: a possible tetragonal distortion to the cubic cell, the existence of a surface impurity layer, vacancy scattering, and structural activation of Raman signal. We use powder X-ray diffraction and confocal Raman spectroscopy with depth profiling to investigate these possibilities and suggest future experiments to explore this phenomenon in more detail. Understanding the lattice dynamics of δ-UO 3 is important for identification of technogenic U phases via Raman and infrared spectroscopy and our results indicate that the simple understanding of δ-UO 3 as a high-symmetry cubic structure should be reconsidered.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2024

Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives

Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, “PolyHighResolution” (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

Non-NASA Center↗
NASA NTRS2023

Microstructural Changes and Pb Mobility During the Zircon to Reidite Transformation: Implications for Planetary Impact Chronology

Impact events modify and leave behind a complex history of rock metamorphism on terrestrial planets. Evidence for an impact event may be recorded in physical changes to minerals, such as mineral deformation and formation of high P-T polymorphs, but also in the form of chemical fingerprints, such as enhanced elemental diffusion and isotopic mixing. Here we explore laboratory shock-induced physical and chemical changes to zircon and feldspar, the former of which is of interest because its trace elements abundances and isotope ratios are used extensively in geochemistry and geochronology. To this end, a granular mixture of Bishop Tuff sanidine and Kuehl Lake zircon, both with well characterized Pb isotope compositions, was prepared and then shocked via a flat plate accelerator. The peak pressure of the experiment, as calculated by the impedance matching method, was ~24 GPa although a broader range of P-T conditions is anticipated due to starting sample porosity. Unshocked and shocked materials were characterized via scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), and Raman spectroscopy. These methods show that the starting zircon material had abundant metamict regions, and the conversion of the feldspar to glass in the post-shock material. Analyses of the shocked product also yielded multiple occurrences of the high-pressure ZrSiO 4 polymorph reidite, with some domains up to 300 μm across. The possibility of U-Pb system disturbance was evaluated via laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and secondary ion mass spectrometry (SIMS). The isotopic data reveal that disturbance of the U-Pb geochronometer in the reidite was minimal (<2% for the main U-Pb geochronometers). To better constrain the P-T conditions during the shock experiment, we complement impedance matching pressure calculations with iSALE2D impact simulations. The simulated results yield a range of P-T conditions experienced during the experiment and show that much of the sample may have reached >30 GPa, which is consistent with formation of reidite. In the recovered shocked material, we identified lamellae of reidite, some of which interlock with zircon lamellae. Reidite {112} twins were identified, which we interpret to have formed to reduce stress between the crystal structure of the host zircon and reidite. These two findings support the interpretation that shear transformation enabled the transition of zircon to reidite. The size and presence of reidite found here indicate that this phase is probably common in impact-shocked crustal rocks that experienced ~25 to ~35 GPa, especially when the target material has porosity. Additionally, shock loading of the zircon and transformation to reidite at these pressures in porous materials is unlikely to significantly disturb the U-Pb system in zircon and that the reidite inherits the primary U and Pb elemental and isotopic ratios from the zircon.

Bishop Tuff↗
DOE OSTI2022

Tackling Disorder in γ‐Ga 2 O 3

Abstract Ga 2 O 3 and its polymorphs are attracting increasing attention. The rich structural space of polymorphic oxide systems such as Ga 2 O 3 offers potential for electronic structure engineering, which is of particular interest for a range of applications, such as power electronics. γ‐Ga 2 O 3 presents a particular challenge across synthesis, characterization, and theory due to its inherent disorder and resulting complex structure–electronic‐structure relationship. Here, density functional theory is used in combination with a machine‐learning approach to screen nearly one million potential structures, thereby developing a robust atomistic model of the γ‐phase. Theoretical results are compared with surface and bulk sensitive soft and hard X‐ray photoelectron spectroscopy, X‐ray absorption spectroscopy, spectroscopic ellipsometry, and photoluminescence excitation spectroscopy experiments representative of the occupied and unoccupied states of γ‐Ga 2 O 3 . The first onset of strong absorption at room temperature is found at 5.1 eV from spectroscopic ellipsometry, which agrees well with the excitation maximum at 5.17 eV obtained by photoluminescence excitation spectroscopy, where the latter shifts to 5.33 eV at 5 K. This work presents a leap forward in the treatment of complex, disordered oxides and is a crucial step toward exploring how their electronic structure can be understood in terms of local coordination and overall structure.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Atomic Structure of the Initial Nucleation Layer in Hexagonal Perovskite BaRuO 3 Thin Films

Hexagonal perovskites are an attractive family of materials due to their various polymorphs and rich structure–property relationships. BaRuO 3 (BRO) is a prototypical hexagonal perovskite, in which the electromagnetic properties are significantly modified depending on its lattice structure. Whereas thin-film synthesis would allow the study of the diverse properties of hexagonal perovskites by epitaxially stabilizing various metastable polymorphs, the epitaxial growth of hexagonal perovskites, especially at the initial growth stage, is yet to be addressed. In this study, it is shown that an intriguing nucleation behavior takes place during the initial stabilization of a hexagonal 9R BRO thin film deposited on a (111) SrTiO 3 (STO) substrate. It is found that a nanoscale strained layer composed of different RuO 6 octahedral stacking is initially formed at the interface followed by a relaxed single crystal 9R BRO thin film. Within the interface layer, hexagonal BRO is nucleated on the (111) STO substrate by both face- and corner-sharing octahedra. More interestingly, it is found that boundaries between differently stacked nucleation layers (heterostructural boundaries) facilitate strain relaxation, in addition to the formation of conventional misfit dislocations evolved from homostructural boundaries. The observations reveal an important underlying mechanism to understand the thin-film epitaxy and strain accommodation in hexagonal perovskites.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Transitional Structures with Continuous Variations in Atomic Positions from Anatase to Rutile Improve Photocatalytic Activity

Abstract TiO 2 polymorphs have distinct properties that are widely employed in various applications. However, mechanisms of transformations between these polymorphs are not fully understood, especially at atomic scale, inhibiting advancing the design and application of the transitional phases. Here, based on results from semi‐in situ transmission electron microscopy, density functional theory, and X‐ray photoemission experiments, a physical picture of transitional structures is discovered, in which continuous variations in atomic positions form along a previously unreported anatase‐to‐rutile phase transformation path of [010] A –to–[] R and (004) A –to– (011) R . These gradient structures give rise to continuous band bending, which promotes electron‐hole separation and inhibits their recombination across the bulk of the particles, leading to a large functionally active volume fraction and resulting in high photoactivity. These findings suggest that interphase matter based on extended gradient structures can be designed to advance new functions not achievable using abrupt interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Quantification of High-Temperature Transition Al2O3 and Their Phase Transformations

High temperature exposure of ?-Al2O3 can lead to a series of polymorphic transformations, including the formation of ?-Al2O3 and ?-Al2O3. Quantification of the microstructure in the ?/?-Al2O3 formation range represents a formidable challenge as both phases accommodate a high degree of structural disorder. In this work, we explore the use of XRD recursive stacking formalism for quantification of high temperature transition aluminas. We formulate the recursive stacking methodology for modelling of disorder in ?-Al2O3 and twinning in ?-Al2O3 and show that explicitly accounting for the disorder is necessary to reliably model the XRD patterns of high temperature transition alumina. In the second part, we use the recursive stacking approach to study phase transformation during high temperature (1050 ºC) treatment. We show that the two different intergrowth modes of ?-Al2O3 have different transformation characteristics, and that a significant portion of ?-Al2O3 is stabilized with ?-Al2O3 even after prolonged high-temperature exposures. In discussions, we outline the limitation of the current XRD approach and discuss a possible multimodal XRD and NMR approach which can improve analysis of complex transition aluminas. This work was performed in the Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by DOEs Office of Biological and Environmental Research and located at PNNL. The work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

Kovarik, Libor↗
DOE OSTI2024

In situ Formation of Platinum-Carbon Catalysts in Propane Dehydrogenation

The catalytic production of propylene via propane dehydrogenation (PDH) is a key reaction in the chemical industry. By combining operando transmission electron microscopy with density functional theory analysis, we show that the intercalation and ordering of carbon on Pt interstitials to form Pt-C solid solutions is relevant for increasing propylene production. More specifically, we found that at the point of enhanced propylene formation, the structure of platinum nanoparticles is transformed into a transient caesium chloride-type Pt-C polymorph. At more elevated temperatures, the zincblende and rock salt polymorphs seemingly coexist. When propylene production was highest, multiple crystal structures consisting of Pt and carbon were occasionally found to coexist in one individual nanoparticle, distorting the Pt lattice. Catalyst coking was detected at all stages of the reaction, but did initially not affect all particles. These findings could lead to the development of novel synthesis strategies towards tailoring highly efficient PDH catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗