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At least 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.

Cohen, Natalie R.↗
DOE OSTI2021

Competing energetic states in γ – Fe 2 W O 6 with strong spin-charge-lattice coupling

We report magnetic and electronic properties of γ – Fe 2 W O 6 via neutron powder-diffraction measurements and first-principles density-function theory calculations. We reveal a magnetic ground state with two phases coexisting in which the minor phase is the same as an earlier report, despite the fact that both materials studied have the same space group but with slightly different atomic positions. Interestingly, both magnetic phases are well captured by first-principles calculations. Furthermore, we show that these two magnetic phases are correlated with electronic properties, with one being insulating and the other being metallic. These features suggest that γ – Fe 2 W O 6 exhibits competing energetic states in which spin, charge, and lattice degrees of freedom are strongly coupled to each other.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Effect of disorder on thermodynamic instability of binary Rare-earth – Nickel – Palladium compounds

In this work, we have investigated the thermodynamic stability of disordered rare-earth phases SmX 2 and Sm 10 X 21 (X=Ni, Pd) using machine-learning based analytical descriptor and first-principles density functional theory methods. The absence of Laves phase compounds in R-Pd binary systems is a longstanding problem of rare earth science: even though Ni and Pd belong to the same group of the periodic table and have similar electronic structure, the Pd compound crystallizes in a monoclinic (C2/m) phase with 10:21 stoichiometry, i.e., Sm 10 Pd 21 , while the Ni compound adopts a cubic Laves phase (MgCu 2 ) structure. To understand this contrasting phase stability, we performed thermodynamic convex hull analysis of Sm x Ni 1-x and Sm x Pd 1-x binary systems, which is experimentally validated using powder X-ray diffraction (PXRD) analyzes of polycrystalline Sm(Ni x Pd 1-x ) 2 samples with x=0, 0.5, and 1. A detailed electronic-structure (band-structure, charge density, and Fermi-surface) analysis of the differences between SmNi 2 /SmPd 2 and Sm 10 Ni 21 /Sm 10 Pd 21 compounds provides the quantum mechanical origin of the unfavorable mixing of Pd with Ni in cubic Laves phase. We show that the stability of Sm-Pd in 10:21 stoichiometry arises from improved intra-/inter-layer 5d-4d bonding compared to the 1:2 stoichiometry. Our work emphasizes the importance of ab-initio methods and computationally inexpensive analytical descriptors for the detailed analysis of thermodynamic and electronic properties of hard-to-prepare rare-earth compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Production of pions, kaons, and protons as a function of the relative transverse activity classifier in pp collisions at $ \sqrt{s} $ = 13 TeV

The production of π ± , K ± , and (p¯)p is measured in pp collisions at √s = 13 TeV in different topological regions of the events. Particle transverse momentum (p T ) spectra are measured in the “toward”, “transverse”, and “away” angular regions defined with respect to the direction of the leading particle in the event. While the toward and away regions contain the fragmentation products of the near-side and away-side jets, respectively, the transverse region is dominated by particles from the Underlying Event (UE). The relative transverse activity classifier, R T = N T / < N T >, is used to group events according to their UE activity, where N T is the measured charged-particle multiplicity per event in the transverse region and < N T > is the mean value over all the analysed events. The first measurements of identified particle p T spectra as a function of R T in the three topological regions are reported. It is found that the yield of high transverse momentum particles relative to the R T -integrated measurement decreases with increasing R T in both the toward and the away regions, indicating that the softer UE dominates particle production as R T increases and validating that R T can be used to control the magnitude of the UE. Conversely, the spectral shapes in the transverse region harden significantly with increasing R T . This hardening follows a mass ordering, being more significant for heavier particles. Finally, it is observed that the pT-differential particle ratios (p+p¯)/(π + +π – ) and (K + + K – )/(π + + π – ) in the low UE limit (R T → 0) approach expectations from Monte Carlo generators such as PYTHIA 8 with Monash 2013 tune and EPOS LHC, where the jet-fragmentation models have been tuned to reproduce e + e – results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Cation-size mismatch as a predictive descriptor for structural distortion, configurational disorder, and valence-band splitting in II-IV-N2 semiconductors

The II-IV-N2 class of heterovalent ternary nitrides has gained significant interest as alternatives to the III-nitrides for electronic and optoelectronic applications. In this study, we apply first-principles calculations based on density functional theory to systematically investigate the effects of structural distortions due to cation size mismatch on the configurational disorder of the cation sublattice and the valence band structure in this class of materials. We find that larger size mismatch between the group-II and the group-IV cations results in stronger lattice distortions from the ideal hexagonal ratio, which in turn inhibits the propensity of these materials toward octet-rule violating cation disorder. We also demonstrate that the formation energy of a single cation antisite pair, which is fast and simple to calculate, is a strong indicator of a material's propensity toward disorder. Furthermore, the breaking of in-plane symmetry leads to a splitting of the top three valence bands at Γ, which is also directly related to the magnitude of structural distortions. Our work demonstrates that the structural and functional properties of the II-IV-N2 materials can be finely tuned through controllable structural distortions that stem from the choice of cations.

Kute, Malhar (ORCID:0000000214364564)↗
DOE OSTI2022

A rotationally invariant approach based on Gutzwiller wave function for correlated electron systems

Here, we introduce a rotationally invariant approach combined with the Gutzwiller conjugate gradient minimization method to study correlated electron systems. In the approach, the Gutzwiller projector is parametrized based on the number of electrons occupying the onsite orbitals instead of the onsite configurations. The approach efficiently groups the onsite orbitals according to their symmetry and greatly reduces the computational complexity, which yields a speedup of $20 \sim 50 \times $ in the minimal basis energy calculation of dimers. The computationally efficient approach promotes more accurate calculations beyond the minimal basis that is inapplicable in the original approach. A large-basis energy calculation of F 2 demonstrates favorable agreements with standard quantum-chemical calculations Bytautas et al (2007 J. Chem. Phys. 127 164317).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils. Five virus isolates, Tunturi 1–5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63–98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils. This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Mixed structures of optical breather and rogue wave for a variable coefficient inhomogeneous fiber system

Breathers and rogue waves are two special types of soliton and play significant role in optical fibers. In this work, the mixed breather and rogue wave solution is constructed for a variable coefficient inhomogeneous fiber system via the Darboux transformation method. The impacts on the mixed wave of the first- and second-order group velocity dispersions (GVD), are discussed, respectively. The spectral eigenvalue parameter control is also studied. The pulse wave width, amplitude and wave density can be controlled by the variable GVD functions and spectral eigenvalue parameter. Especially, two types of rogue wave solutions can be derived from the mixed solution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Separation of life stages within anaerobic fungi (Neocallimastigomycota) highlights differences in global transcription and metabolism

Anaerobic gut fungi of the phylum Neocallimastigomycota are microbes proficient in valorizing low-cost but difficult-to-breakdown lignocellulosic plant biomass. Characterization of different fungal life stages and how they contribute to biomass breakdown are critical for biotechnological applications, yet we lack foundational knowledge about the transcriptional, metabolic, and enzyme secretion behavior of different life stages of anaerobic gut fungi: zoospores, germlings, immature thalli, and mature zoosporangia. A Miracloth-based technique was developed to enrich cell pellets with zoospores - the free-swimming, flagellated, young life stage of anaerobic gut fungi. By contrast, fungal mats contained relatively more vegetative, encysted, mature sporangia that form films. Global gene expression profiles were compared from two sample types (zoospore-enriched cell pellets vs. mature mats) harvested from the anaerobic gut fungal strain Neocallimastix californiae G1. Despite cultures being grown on glucose, the fungal zoospore-enriched samples were transcriptionally primed to encounter plant matter substrate, as evidenced by upregulation of catabolic carbohydrate-active enzymes and putative carbohydrate transporters. Furthermore, we report significant differential gene expression for gene annotation groups, including putative secondary metabolites and transcription factors. Understanding global gene expression differences between the fungal zoospore-enriched cells and mature fungi aid in characterizing fungal development, unmasking gene function, and guiding cultivation conditions and engineering targets to promote enzyme secretion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An arbitrarily high-order three-dimensional Cartesian-grid method for reconstructing interfaces from volume fraction fields

Here Tthis work describes a newly developed, arbitrarily high-order Cartesian-grid method for reconstructing material interfaces from a volume fraction field. The method begins by identifying all of the grid cells in the volume fraction field that are intersected by the interface and need to be approximated by the reconstruction scheme. Finite-differences are used to calculate the gradient of the volume fraction field and provide an estimate of the surface normal in all of the interfacial grid cells. Groups of connected grid cells are then identified which all have the same dominant component of the normal vector. This grouping by orientation determines the proper dependent variable to use in the surface reconstruction (e.g. for a 2D curve, this step determines if the surface will be approximated by a function of x or y). A cumulative integral over the surface is constructed and fit using b-splines for two-dimensional problems or tensor-product b-splines for three-dimensional problems. This construction allows for the interface to be recovered through application of the second fundamental theorem of calculus. Fitting the cumulative integral with $\mathscr{N}$ th-order b-splines (or tensor-product b-splines) yields an ($\mathscr{N}$-1) th-order convergence rate of the interface shape. Differentiation of the b-spline interface function(s) allows for the high-order approximation of the normal vector and curvature to be obtained directly anywhere along b-spline. Together, the proposed reconstruction technique can achieve arbitrarily high mesh convergence rates. Validation tests are presented with mesh convergence rates ranging from fourth- to tenth-order.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Postsynthetic Oxidation of the Coordination Site in a Heterometallic Metal-Organic Framework: Tuning Catalytic Behaviors

Postsynthetic modification (PSM) in metal-organic frameworks (MOFs) can introduce multiple functionalities and alter the structural function for the desired application. However, the PSM of the coordination site faces the challenges of structural collapse or incompatibility between the original metal site and the newly formed coordination group. Herein, we developed a novel concept of introducing “primary” and “secondary” nodes, coexisting in a water-stable, Zr-based heterometallic MOF, [Zr6(µ3-OH)8(OH)8][CuI4(L1)4]2 (1-SH-a, H2L1 = 6-mercaptopyridine-3-carboxylic acid). The post-synthetic oxidation at the coordination site was successfully achieved in the “secondary” nodes [CuI4(L1)4]4-, while the robust “primary” nodes [Zr6(µ3-OH)8(OH)8]8+ stabilized the whole framework to form [Zr6(µ3-OH)8(OH)8][(CuI0.44CuII0.56(OH)0.56)4(L2)4]2 (1-SO3H, H2L2 = 6-sulfonicotinic acid). PSM of 1-SH-a to form 1-SO3H dramatically tuned the catalytic properties toward the styrene oxide ring-opening reaction to give a regioselectivity of primary alcohol (A) of ~99% compared with 1-SH-a (~71%).

Han, Yi↗
DOE OSTI2022

Structural and Electronic Effect Driven Distortions in Visible Light Absorbing Polar Materials A Ta 2 V 2 O 11 ( A = Sr, Pb)

Complex vanadates of tantalum(V), such as ATa 2 V 2 O 11 (A = Sr, Pb), are rare and underrated materials, which have potential application domains that could be substantially expanded, mitigating the existing controversy on their atomic and electronic organization. Herein, we present a thorough structural examination combining synchrotron powder X-ray diffraction-aided distortion mode analysis with computational methods to study hettotypes of SrTa 2 V 2 O 11 (STVO) and PbTa 2 V 2 O 11 (PTVO). Being distinct from the perovskite family due to the presence of [VO 4 ] groups, both compounds are polar dielectric materials with certain similarities to SBT and PBT Aurivillius phases. Applying the model of anions of metallic matrices to the analysis of electron localization functions calculated on top of as-established equilibrium structures helps retrace the effects in the Sr and Pb surroundings on the respective crystal packings of STVO and PTVO.

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

Intermetallic Nanocatalysts from Heterobimetallic Group 10–14 Pyridine-2-thiolate Precursors

Intermetallic compounds are atomically ordered inorganic materials containing two or more transition metals and main-group elements in unique crystal structures. Intermetallics based on group 10 and group 14 metals have shown enhanced activity, selectivity, and durability in comparison to simple metals and alloys in many catalytic reactions. While high-temperature solid-state methods to prepare intermetallic compounds exist, softer synthetic methods can provide key advantages, such as enabling the preparation of metastable phases or of smaller particles with increased surface areas for catalysis. In this work, we study a generalized family of heterobimetallic precursors to binary intermetallics, each containing a group 10 metal and a group 14 tetrel bonded together and supported by pincer-like pyridine-2-thiolate ligands. Upon thermal decomposition, these heterobimetallic complexes form 10–14 binary intermetallic nanocrystals. Experiments and density functional theory (DFT) computations help in better understanding the reactivity of these precursors toward the synthesis of specific intermetallic binary phases. Using Pd 2 Sn as an example, we demonstrate that nanoparticles made in this way can act as uniquely selective catalysts for the reduction of nitroarenes to azoxyarenes, which highlights the utility of the intermetallics made by our method. Employing heterobimetallic pincer complexes as precursors toward binary nanocrystals and other metal-rich intermetallics provides opportunities to explore the fundamental chemistry and applications of these materials.

10-14 intermetallics↗
DOE OSTI2020

Luminescent Properties of DOBDC Containing MOFs: The Role of Free Hydroxyls

A novel metal–organic framework (MOF), Mn-DOBDC, has been synthesized in an effort to investigate the role of both the metal center and presence of free linker hydroxyls on the luminescent properties of DOBDC (2,5-dihydroxyterephthalic acid) containing MOFs. Co-MOF-74, RE-DOBDC (RE–Eu and Tb), and Mn-DOBDC have been synthesized and analyzed by powder X-ray diffraction (PXRD) and the fluorescent properties probed by UV–Vis spectroscopy and density functional theory (DFT). Mn-DOBDC has been synthesized by a new method involving a concurrent facile reflux synthesis and slow crystallization, resulting in yellow single crystals in monoclinic space group C2/c. Mn-DOBDC was further analyzed by single-crystal X-ray diffraction (SCXRD), scanning electron microscopy–energy-dispersive spectroscopy (SEM-EDS), and photoluminescent emission. Results indicate that the luminescent properties of the DOBDC linker are transferred to the three-dimensional structures of both the RE-DOBDC and Mn-DOBDC, which contain free hydroxyls on the linker. In Co-MOF-74 however, luminescence is quenched in the solid state due to binding of the phenolic hydroxyls within the MOF structure. Finally, Mn-DOBDC exhibits a ligand-based tunable emission that can be controlled in solution by the use of different solvents.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Homo- and hetero-dimeric subunit interactions set affinity and efficacy in metabotropic glutamate receptors

Metabotropic glutamate receptors (mGluRs) are dimeric class C G-protein–coupled receptors that operate in glia and neurons. Glutamate affinity and efficacy vary greatly between the eight mGluRs. The molecular basis of this diversity is not understood. We used single-molecule fluorescence energy transfer to monitor the structural rearrangements of activation in the mGluR ligand binding domain (LBD). In saturating glutamate, group II homodimers fully occupy the activated LBD conformation (full efficacy) but homodimers of group III mGluRs do not. Strikingly, the reduced efficacy of Group III homodimers does not arise from differences in the glutamate binding pocket but, instead, from interactions within the extracellular dimerization interface that impede active state occupancy. By contrast, the functionally boosted mGluR II/III heterodimers lack these interface ‘brakes’ to activation and heterodimer asymmetry in the flexibility of a disulfide loop connecting LBDs greatly favors occupancy of the activated conformation. Our results suggest that dimerization interface interactions generate substantial functional diversity by differentially stabilizing the activated conformation. This diversity may optimize mGluR responsiveness for the distinct spatio-temporal profiles of synaptic versus extrasynaptic glutamate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Uncertainty-aware mixed-variable machine learning for materials design

Abstract Data-driven design shows the promise of accelerating materials discovery but is challenging due to the prohibitive cost of searching the vast design space of chemistry, structure, and synthesis methods. Bayesian optimization (BO) employs uncertainty-aware machine learning models to select promising designs to evaluate, hence reducing the cost. However, BO with mixed numerical and categorical variables, which is of particular interest in materials design, has not been well studied. In this work, we survey frequentist and Bayesian approaches to uncertainty quantification of machine learning with mixed variables. We then conduct a systematic comparative study of their performances in BO using a popular representative model from each group, the random forest-based Lolo model (frequentist) and the latent variable Gaussian process model (Bayesian). We examine the efficacy of the two models in the optimization of mathematical functions, as well as properties of structural and functional materials, where we observe performance differences as related to problem dimensionality and complexity. By investigating the machine learning models’ predictive and uncertainty estimation capabilities, we provide interpretations of the observed performance differences. Our results provide practical guidance on choosing between frequentist and Bayesian uncertainty-aware machine learning models for mixed-variable BO in materials design.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Dimensional reduction upon calcium incorporation in Cs 0.3 (Ca 0.3 Ln 0.7 )PS 4 and Cs 0.5 (Ca 0.5 Ln 0.5 )PS 4

A series of Ca-containing lanthanide thiophosphates has been obtained and their structural evolution from 3D for LnPS 4 and Cs 0.3 (Ln 0.7 Ca 0.3 )PS 4 to 2D in Cs 0.5 (Ln 0.5 Ca 0.5 )PS 4 was shown as a function of Ca content. The first series with an idealized formula of Cs 0.3 (Ca 0.3 Ln 0.7 )PS 4 crystallizes in the R3¯m with combining macron]m space group and belongs to a new structure type that consists of a channel containing [(Ca 0.3 Ln 0.7 )PS 4 ] 0.3– framework, where the channels are occupied by severely disordered Cs + cations. A second new series with formula Cs 0.5 (Ca 0.5 Ln 0.5 )PS 4 crystallizes in the monoclinic C2/c space group and exhibits a layered structure consisting of [(Ca 0.5 Ln 0.5 )PS 4 ] 0.5– layers with Cs + cations located between the layers for charge balance. Together with the parent structure type, LnPS 4 , these three structure types illustrate how the LnPS 4 structure changes with Cs + cation incorporation, reducing its dimensionality from 3D to 2D. The magnetic properties of Cs 0.3 [(Ca 0.3 Ce 0.7 )PS 4 ] and Cs 0.3 [(Ca 0.3 Pr 0.7 )PS 4 ] were studied and revealed no magnetic transition down to 2 K.

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

Hydration of α-UO 3 following storage under controlled conditions of temperature and relative humidity

Changes in chemical speciation of uranium oxides following storage under varied conditions of temperature and relative humidity are valuable for characterizing material provenance. In this study, subsamples of high purity α-UO 3 were stored under four sets of controlled conditions of temperature and relative humidity over several years, and then measured periodically for chemical speciation. Powder X-ray diffraction (XRD) analysis and extended X-ray absorption fine structure spectroscopy confirm hydration of α-UO 3 to a schoepite-like end product following storage under each of the varied storage conditions, but the species formed during exposure to the lower relative humidity and lower temperature condition follows different trends from those formed under the other three storage conditions (high relative humidity with high or low temperatures, and low relative humidity with a high temperature). Thermogravimetry coupled with XRD analysis was carried out to distinguish desorption pathways of water from the hydrated end products. Density functional theory calculations discern changes in the structure of α-UO 3 following incorporation of 1, 2 or 3 H 2 O molecules or 1, 2 or 3 OH groups into the orthorhombic lattice, revealing differences in lattice constants, U–O bond lengths, and U–U distances. The collective results from this analysis are in contrast to analogous studies that report that U 3 O 8 is oxidized and hydrated in air during storage under high relative humidity conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗