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At least 1,567 records · Page 87

Prediction of vacancy defect diffusion paths in high entropy alloys via machine learning on molecular dynamics data

Identifying the diffusion path of point defects is a critical step in understanding their evolution and the mechanisms of related phenomena. Defect diffusion occurs at small length and time scales, with impacts on material properties that may continue to evolve over ns to μs, ms, and the continuum scale (s, min, etc., and cm, m, etc.). The time scale accessible to molecular dynamics (MD) simulations is limited by small step sizes, typically in the fs range. Thus, surrogate models of MD simulations through machine learning (ML)-based algorithms are of great interest, especially for complex systems such as high entropy alloys (HEAs). In this work, dynamics governing vacancy migration in HEA were approximated with graph convolutional network (GCN) models as ansatzes for kinetic Monte Carlo (KMC) rate catalogs. Network design considered that diffusion in crystalline solids generally depends on interactions between defects and their immediate neighbor atoms. Graphs represented the vacancy surroundings, MD-generated trajectories provided training and comparison datasets, and unsupervised GCN models approximated interatomic dynamics governing vacancy migration in HEAs as ansatzes for KMC. A proof-of-concept model trained on MD data for the Fe, Ni, Cr, Co, and Cu HEA environment was used with two different neighbor interactions to assess the feasibility of training a GCN to predict vacancy defect transition rates in the HEA environment. The resulting setup rapidly generated MD-formatted synthetic trajectories based on dynamics learned from the MD training set, with a time acceleration of roughly two orders of magnitude and a similar diffusion coefficient to MD observations. Additionally, Nudged Elastic Band (NEB) calculations were performed on randomly generated FeNiCrCoCu HEA structures to determine vacancy migration barriers across nearest-neighbor sites. Transition probabilities for each jump, categorized by atomic type, were extracted from these calculations. NEB-based and GCN-based approaches led to similar outcomes.

Reimer, C↗

Extreme elevational migration spurred cryptic speciation in giant hummingbirds

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how “outlier” species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world’s largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.

Science & Technology - Other Topics↗

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO 2 in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate (HCO$^–_3$), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic β-carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO$^–_3$ relative to CO 2 . To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO 2 -concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO 2 assimilation in a crowded model carboxysome. Despite a relatively high CO 2 permeability of approximately 10 -2 cm/s across the carboxysome shell, the shell proteins reflect enough CO 2 back toward rubisco that 2,650 CO 2 molecules can be fixed by rubisco for every 1 CO 2 molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.

59 BASIC BIOLOGICAL SCIENCES↗

Discovery and characterization of two Neptune-mass planets orbiting HD 212729 with TESS

ABSTRACT We report the discovery of two exoplanets orbiting around HD 212729 (TOI 1052, TIC 317060587), a Teff = 6146 K star with V = 9.51 observed by TESS in Sectors 1 and 13. One exoplanet, TOI-1052b, is Neptune-mass and transits the star, and an additional planet TOI-1052c is observed in radial velocities but not seen to transit. We confirm the planetary nature of TOI-1052b using precise radial velocity observations from HARPS and determined its parameters in a joint RV and photometry analysis. TOI-1052b has a radius of $2.87^{+0.29}_{-0.24}$ R⊕, a mass of 16.9 ± 1.7 M⊕, and an orbital period of 9.14 d. TOI-1052c does not show any transits in the TESS data, and has a minimum mass of $34.3^{+4.1}_{-3.7}$ M⊕ and an orbital period of 35.8 d, placing it just interior to the 4:1 mean-motion resonance. Both planets are best fit by relatively high but only marginally significant eccentricities of $0.18^{+0.09}_{-0.07}$ for planet b and $0.24^{+0.09}_{-0.08}$ for planet c. We perform a dynamical analysis and internal structure model of the planets as well as deriving stellar parameters and chemical abundances. The mean density of TOI-1052b is $3.9^{+1.7}_{-1.3}$ g cm−3 consistent with an internal structure similar to Neptune. A nearby star is observed in Gaia DR3 with the same distance and proper motion as TOI-1052, at a sky projected separation of $\scriptstyle \sim$1500 au, making this a potential wide binary star system.

Armstrong, David J. (ORCID:0000000250804117)↗

Heterostructural interface engineering for ultrawide-gap nitrides from first principles: Ta C / Al N and Ta C / Ga N rocksalt-wurtzite interfaces

Epitaxial lattice matching is an important condition for the formation of coherent interfaces with low defect densities. However, lattice-matched substrates with the same crystal structure as the active layer are often not available, suggesting opportunities for utilizing heterostructural interfaces. For example, at high Al contents that are interesting for ultrawide-gap applications in power electronics, Al x ⁢Ga 1-x ⁢N semiconductor alloys in the (0001) orientation of the wurtzite (wz) structure become lattice-matched to (111)-oriented rocksalt (rs) Ta⁢C substrates. To predict the expected interface atomic structures under different synthesis conditions, we perform high-throughput density-functional-theory calculations, using an algorithm for systematic sampling of the possible stacking sequences of the atomic layers on the in-plane hexagonal lattice. The approach considers octahedral, tetrahedral, and prismatic coordination motifs, and is generally applicable for the modeling of commensurate rs/wz heterostructural interfaces. Our results provide guidance for synthesis control of substrate-film bonding and the polarity of ultrawide-gap Al x⁢ Ga 1-x⁢ N alloys on Ta⁢C substrates.

36 MATERIALS SCIENCE↗

Pressure-induced suppression of ferromagnetism in the itinerant ferromagnet LaCrSb 3

We have performed an extensive pressure-dependent structural, spectroscopic, and electrical transport study of LaCrSb 3 . The ferromagnetic phase (TC=120 K at p = 0 GPa) is fully suppressed by p = 26.5 GPa and the Cr moment decreases steadily with increasing pressure. The unit-cell volume decreases smoothly up to p = 55 GPa. We find that the bulk modulus and suppression of the magnetism are in good agreement with theoretical predictions, but the Cr moment decreases smoothly with pressure, in contrast to steplike drops predicted by theory. The ferromagnetic ordering temperature appears to be driven by the Cr moment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Paramagnon dispersion and damping in doped Na x Ca 2 – x CuO 2 Cl 2

Here, using resonant inelastic x-ray scattering, we measure the paramagnon dispersion and damping of undoped, antiferromagnetic Ca 2 CuO 2 Cl 2 as well as doped, superconducting Na x Ca 2–x CuO 2 Cl 2 . Our estimation of the spin-exchange parameter and width of the paramagnon peak at the zone boundary X=(0.5, 0) confirms that no simple relation can be drawn between these parameters and the critical temperature T c . Consistently with other cuprate compounds, we show that upon doping there is a slight softening at (0.25,0) but not at the zone boundary X. In combination with these measurements we perform calculations of the dynamical spin structure factor of the one-band Hubbard model using cluster dynamical mean-field theory. The calculations are in excellent agreement with the experiment in the undoped case, both in terms of energy position and width. While the increase in width is also captured upon doping, the dynamical spin structure factor shows a sizable softening at X, which provides insightful information on the length-scale of the spin fluctuations in doped cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

From Trivial Kondo Insulator Ce 3 Pt 3 Bi 4 to Topological Nodal-Line Semimetal Ce 3 Pd 3 Bi 4

In this work, using the density functional theory combined with dynamical mean-field theory, we have performed systematic study of the electronic structure and its band topology properties of Ce 3 Pt 3 Bi 4 and Ce 3 Pd 3 Bi 4 . At high temperatures ( ~ 290 K ), the electronic structures of both compounds resemble the open-core 4 f density functional calculation results. For Ce 3 Pt 3 Bi 4 , clear hybridization gap can be observed below 72 K, and its coherent momentum-resolved spectral function below 18 K exhibits an topologically trivial indirect gap of ~ 6 meV and resembles density functional band structure with itinerant 4 f state. For Ce 3 Pd 3 Bi 4 , no clear hybridization gap can be observed down to 4 K, and its momentum-resolved spectral function resembles electron-doped open-core 4 f density functional calculations. The band nodal points of Ce 3 Pd 3 Bi 4 at 4 K are protected by the gliding-mirror symmetry and form ringlike structure. Therefore, the Ce 3 Pt 3 Bi 4 compound is topologically trivial Kondo insulator while the Ce 3 Pd 3 Bi 4 compound is topological nodal-line semimetal.

36 MATERIALS SCIENCE↗

First-principles comparative study of Cr migration in O3 and O/P hybrid-phased NaCrO 2

In layered Na transition-metal (TM) oxides, TM migration usually occurs at highly charged states and severely deteriorates the capacity and reversibility. Meanwhile, the formation of hybrid phases with the intergrowth of octahedral (O-type) and prismatic (P-type) Na layers also takes place at highly charged states. These hybrid phases are often more stable than simple O3 or P3 stackings. However, little is known about the mechanism and impact of TM migration in these hybrid phases. In this work, a comparative first-principles study is performed to understand the connections between structural changes and Cr migration in layered O3 and hybrid-phased NaCrO 2 . After Cr migration, the hybrid-phased NaCrO 2 suffers from greater layer shrinkage than the O3 phase. Three factors affect the Cr migration energy E mig : the Na concentration, local 3D configurations, and 2D in-plane geometries. Low Na concentrations and certain local 3D configurations facilitate the Cr migration. The Cr migration barriers in both O3 and hybrid-phased NaCrO 2 are positively correlated with the Cr E mig . The Cr migration in 17 doped O3 and hybrid-phased NaCrO 2 is surveyed. In these doped NaCrO 2 , a more uniform distribution of the Cr–O bond lengths usually suggests suppressed Cr migration. Optimal dopants for suppressing Cr migration are identified by considering E mig for both Cr and the dopant. Finally, our comparative study on Cr migration in O3 and hybrid-phased NaCrO 2 reveals the significant role of hybrid-phased structures in the development of layered cathode materials.

36 MATERIALS SCIENCE↗

Observation of structures in the J/ψ+ψ(2S) mass spectrum with the ATLAS detector

A search for resonant structures in the mass spectrum is performed using proton-proton collision data at , corresponding to an integrated luminosity of , recorded by the ATLAS experiment at the LHC. The decay channels of and are analyzed. An excess near 6.9 GeV is observed in both channels with a combined significance of . No significant signal is observed near 7.2 GeV, and an upper limit on its yield relative to is provided. A simultaneous fit with the di- channel is carried out under assumptions regarding the resonance interferences, yielding a ratio of the partial decay widths between the and di- channels of for the resonance near 6.9 GeV.

Aad, G↗

Lead-chelating hole-transport layers for efficient and stable perovskite minimodules

The defective bottom interfaces of perovskites and hole-transport layers (HTLs) limit the performance of p-i-n structure perovskite solar cells. We report that the addition of lead chelation molecules into HTLs can strongly interact with lead(II) ion (Pb 2+ ), resulting in a reduced amorphous region in perovskites near HTLs and a passivated perovskite bottom surface. Here, the minimodule with an aperture area of 26.9 square centimeters has a power conversion efficiency (PCE) of 21.8% (stabilized at 21.1%) that is certified by the National Renewable Energy Laboratory (NREL), which corresponds to a minimal small-cell efficiency of 24.6% (stabilized 24.1%) throughout the module area. Small-area cells and large-area minimodules with lead chelation molecules in HTLs had a light soaking stability of 3010 and 2130 hours, respectively, at an efficiency loss of 10% from the initial value under 1-sun illumination and open-circuit voltage conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE JGI Metagenome Workflow

The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751–D763, 2021, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723–D733, 2021, https://doi.org/10.1093/nar/gkaa983).

59 BASIC BIOLOGICAL SCIENCES↗

Parallel Randomized Tucker Decomposition Algorithms

The Tucker tensor decomposition is a natural extension of the singular value decomposition (SVD) to multiway data. Here, we propose to accelerate Tucker tensor decomposition algorithms by using randomization and parallelization. We present two algorithms that scale to large data and many processors, significantly reduce both computation and communication cost compared to previous deterministic and randomized approaches, and obtain nearly the same approximation errors. The key idea in our algorithms is to perform randomized sketches with Kronecker-structured random matrices, which reduces computation compared to unstructured matrices and can be implemented using a fundamental tensor computational kernel. We provide probabilistic error analysis of our algorithms and implement a new parallel algorithm for the structured randomized sketch. Our experimental results demonstrate that our combination of randomization and parallelization achieves accurate Tucker decompositions much faster than alternative approaches. We observe up to a 16X speedup over the fastest deterministic parallel implementation on 3D simulation data.

Tucker decompositions↗

ProFAST (Production Financial Analysis Scenario Tool) [SWR-23-88]

The Production Financial Analysis Scenario Tool (ProFAST) provides a quick and convenient in-depth financial analysis for production facilities. The model uses a generally accepted accounting principles analysis framework and provides annual projections of income statements, cash flow statements, and balance sheets. ProFAST allows users to calculate the levelized cost of the produced commodity by providing an expected financial performance, or on the other hand, calculate the financial performance based on an input price. Model inputs generally capital expenditures, operating expenditures, and financing structure. The programmatic approach of ProFAST allows users to easily perform large sensitivity analyses and integrates easily with other python tools.

Kee, Jamie↗

Interpretable, Extensible Linear Regression Model for Electron Density Prediction

This code allows us to generate a model to predict ground state electron densities directly from atomic structure thereby bypassing the need to perform direct DFT calculations. It is based on many body correlation descriptors defined in https://arxiv.org/abs/2004.14442 (IM release numbers: LLNL-JRNL- 808791 and LLNL-JRNL-840698). The code reads in electron densities, in CHGCAR format used by the DFT code VASP, calculates many-body correlation descriptors based on atoms surrounding a grid point and then uses linear regression to obtain the fitting parameters.

Kumar, Shashikant↗

Triso Analysis Tool For Predictive Source Terms

Source term modeling for TRi-structural ISOtropic (TRISO) fuel has been performed for previous reactor designs, but few are available in the open literature. Thus, there is a need to develop a simple, versatile, and mechanistic model of fission product release and transport in gas reactor cores that can be applied to a variety of reactors through user inputs and reactor-specific radionuclide inventories. To meet this need, the TRISO Analysis Tool for Predictive Source terms (TRISO-ATOPS) was developed. This model calculates the release of the key safety-important fission products by diffusion through the kernel, silicon carbide and graphite based on fuel and graphite temperatures in the reactor under normal operation. These releases from the fuel enter the coolant where they can plate-out on cooler surfaces. A clean-up model is included for designs with a coolant purification system for removing fission gases. This initial distribution of fission products in the reactor serves as an initial condition for potential releases under postulated accident conditions. From this initial condition, the model calculates the fission product release for any transient temperature profile, and the fission product releases can then be used to assess radiological dose to the workers and the public using conventional radiological dose tools. Data on the diffusion of fission products is based on historic German TRISO experiments and the more current Department of Energy Advanced Gas Reactor TRISO fuel development program. The example cases in this work demonstrate the flexibility of the model

Stoyer, Benjamin [Idaho National Laboratory (INL),↗

buhito

buhito is a Python library for graph analysis and machine learning. Graphs can represent networks with objects as nodes and their relationships as edges. buhito focuses on graphlet methods that study graphs through enumerating their component subgraphs to enable interpretable and fast models of complex systems. The package provides tools for different algorithmic designs for computing, analyzing, and applying graphlets to research problems such as machine learning, data compression, and anomaly detection in graph-structured data. A central feature is performing decomposition data analysis on graphs for machine learning models. Implemented in Python and built upon open-source scientific libraries such as NetworkX, NumPy, and SciPy, buhito provides high-performance methods for researchers exploring the mathematical and computational foundations of graphlet analysis applicable to systems of different sizes.

Pimonova, Yulia↗

Data for Impact of Non-Irrigation on 1G and 2G Bioethanol Potential of Oilcane Feedstock: A Field to Fuel Pipeline Study

This study evaluates the bioethanol potential in response to irrigation (IR) and non-irrigation (NIR) of oilcane (OC) during a seasonal drought prior harvest. The juice was extracted through mechanical pressing of stems and fermented by Ethanol Red® yeast to produce first-generation bioethanol. Hydrothermal pretreatment followed by enzymatic hydrolysis of bagasse was performed to produce monomeric sugars from structural carbohydrates. The hydrolysates were fermented with engineered yeast for second-generation bioethanol production. The irrigated oilcane juice (276.3 ± 8.9 g/L) constitutes higher sugar concentrations than non-irrigated oilcane juice (236.5 ± 2.2 g/L). The enzymatic hydrolysis of IR-OC and NIR-OC pretreated bagasse yielded similar concentrations of 247.5 ± 2.22 and 249.7 ± 4.98 g/L fermentable sugars. Industry-relevant bioethanol titers of ≥99 g/L and ≥75 g/L were achieved from juice and hydrolysates, respectively. Therefore, the non-irrigation regime did not impact the 1G and 2G bioethanol titers. However, the overall bioethanol yield can be lower due to the reduction of stem yield (8 %) per hectare.

Biomass Analytics↗