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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Efficient machine learning interatomic potentials robust for liquid and multiple solid polymorphs of NaF and KF

Achieving atomic-level understanding of crystallization of molten salts is of importance to a wide range of technological applications. Recent work [Fan et al., Proc. Natl. Acad. Sci. USA 122, e2425702122 (2025)] revealed that crystal nucleation in molten LiF salt is a multistage process according to the molecular-dynamics (MD) simulations based on an atomic cluster expansion (ACE) machine-learning interatomic potential (MLIP). In order to understand the influence of increasing cation size on nucleation pathways and nucleation rates of molten fluoride salts, here we develop two new ACE MLIPs for NaF and KF. The two ACE MLIPs feature DFT-SCAN-level accuracy for liquid and multiple solid polymorphs over a wide temperature (0–2000 K) and pressure (0–100 GPa) range, and also reproduce well a number of experimental data for solid and liquid equilibrium properties. The efficiency of the two ACE MLIPs enable million-atom-scale or microsecond-scale MD simulations. The two general-purpose ACE MLIPs are expected to be useful for atomistic simulations for different purposes, in addition to studying crystallization of molten NaF and KF salts.

Crystal melting↗
DOE OSTI2022

Crystal structure of a trigonal polymorph of aquadioxidobis(pentane-2,4-dionato-κ 2 O , O ′)uranium(VI)

The title compound, [UO 2 (acac) 2 (H 2 O)] consists of a uranyl(VI) unit ([O=U=O] 2+ ) coordinated to two monoanionic acetylacetonate (acac, C 5 H 7 O 2 ) ligands and one water molecule. The asymmetric unit includes a one-half of a uranium atom, one oxido ion, one-half of a water molecule and one acac ligand. The coordination about the uranium atom is distorted pentagonal–bipyramidal. The acac ligands and O w atom comprise the equatorial plane, while the uranyl O atoms occupy the axial positions. Intermolecular hydrogen bonding between complexes results in the formation of two-dimensional hexagonal void channels along the c- axis direction with a diameter of 6.7 Å. The monoclinic ( P 2 1 / c space group) polymorph was reported by Alcock & Flanders [(1987). Acta Cryst. C 43 , 1480–1483].

Hernandez, Alejandro↗
DOE OSTI2020

CHRNA5 rs16969968 polymorphism is associated with lung cancer risk: A meta‐analysis

Abstract Objective To evaluate the genetic association between rs16969968 and lung cancer risk by meta‐analysis. Data source We searched eligible studies from MEDLINE, Web of Science and EMBASE up to Dec, 2017. Study selection Association studies concerning rs16969968 and lung cancer risk were included. We assessed the association strength between this polymorphism and risk of lung cancer by calculating odds ratios (OR) and 95% confidence interval (95%CI). Results A total of 26 data sets comprising 30 772 lung cancers and 90 954 controls were included. rs16969968 was found to be associated with lung cancer risk in population of European ancestry in all models (A vs. G: OR = 1.30, 95%CI 1.27‐1.33, P < 0.001; AA + GA vs. GG: OR = 1.38, 95%CI 1.33‐1.43, P < 0.001; AA vs. GG + GA: OR = 1.45, 95%CI 1.38‐1.53, P < 0.001), consistent with previous genome‐wide association study (GWAS). However, no association was observed in Asians (A vs. G: OR = 1.19. 95%CI 0.95‐1.49, P = 0.131). The minor allele A may increase the risk of lung cancer in both smokers (OR = 1.33, 95%CI 1.29‐1.39, P < 0.001) and nonsmokers (OR = 1.25, 95%CI 1.12‐1.39, P < 0.001). There was no obvious publication bias in all analyses. Conclusions Our analysis provided more evidence that rs16969968 is a susceptibility locus of lung cancer in the Caucasians and that it may be not associated with the risk in the Asians.

Zhou, Wei↗
DOE OSTI2022

A MUC 5 B Gene Polymorphism, rs35705950-T, Confers Protective Effects Against COVID-19 Hospitalization but Not Severe Disease or Mortality

A common MUC5B gene polymorphism, rs35705950-T, is associated with idiopathic pulmonary fibrosis (IPF), but its role in severe acute respiratory syndrome coronavirus 2 infection and disease severity is unclear. To assess whether rs35705950-T confers differential risk for clinical outcomes associated with coronavirus disease (COVID-19) infection among participants in the Million Veteran Program (MVP). The MUC5B rs35705950-T allele was directly genotyped among MVP participants; clinical events and comorbidities were extracted from the electronic health records. Associations between the incidence or severity of COVID-19 and rs35705950-T were analyzed within each ancestry group in the MVP followed by transancestry meta-analysis. Replication and joint meta-analysis were conducted using summary statistics from the COVID-19 Host Genetics Initiative (HGI). Sensitivity analyses with adjustment for additional covariates (body mass index, Charlson comorbidity index, smoking, asbestosis, rheumatoid arthritis with interstitial lung disease, and IPF) and associations with post–COVID-19 pneumonia were performed in MVP subjects. The MUC5B variant rs35705950-T may confer protection in COVID-19 hospitalizations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Contact-dependent growth inhibition (CDI) systems deploy a large family of polymorphic ionophoric toxins for inter-bacterial competition

Contact-dependent growth inhibition (CDI) is a widespread form of inter-bacterial competition mediated by CdiA effector proteins. CdiA is presented on the inhibitor cell surface and delivers its toxic C-terminal region (CdiA-CT) into neighboring bacteria upon contact. Inhibitor cells also produce CdiI immunity proteins, which neutralize CdiA-CT toxins to prevent auto-inhibition. Here, we describe a diverse group of CDI ionophore toxins that dissipate the transmembrane potential in target bacteria. These CdiA-CT toxins are composed of two distinct domains based on AlphaFold2 modeling. The C-terminal ionophore domains are all predicted to form five-helix bundles capable of spanning the cell membrane. The N-terminal "entry" domains are variable in structure and appear to hijack different integral membrane proteins to promote toxin assembly into the lipid bilayer. The CDI ionophores deployed by E. coli isolates partition into six major groups based on their entry domain structures. Comparative sequence analyses led to the identification of receptor proteins for ionophore toxins from groups 1 & 3 (AcrB), group 2 (SecY) and groups 4 (YciB). Using forward genetic approaches, we identify novel receptors for the group 5 and 6 ionophores. Group 5 exploits homologous putrescine import proteins encoded by puuP and plaP, and group 6 toxins recognize di/tripeptide transporters encoded by paralogous dtpA and dtpB genes. Finally, we find that the ionophore domains exhibit significant intra-group sequence variation, particularly at positions that are predicted to interact with CdiI. Accordingly, the corresponding immunity proteins are also highly polymorphic, typically sharing only ~30% sequence identity with members of the same group. Competition experiments confirm that the immunity proteins are specific for their cognate ionophores and provide no protection against other toxins from the same group. The specificity of this protein interaction network provides a mechanism for self/nonself discrimination between E. coli isolates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of Chlamydia and may better inform rational vaccine design and functional studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

LiMnO2 polymorphs

Energies of LiMnO2 polymorphs computed within various DFT approximations

36 MATERIALS SCIENCE↗
DOE OSTI2024

An empirical DNA-based identification of morphologically similar snappers (Lutjanus campechanus, Lutjanus purpureus) using a versatile bioinformatics workflow for the discovery and analysis of informative single-nucleotide polymorphisms

The commercially important speciesLutjanus campechanus(Northern/Gulf red snapper) andLutjanus purpureus(Southern/Caribbean red snapper) are the protagonists of a decade’s long taxonomic debate over their species delimitation, due in part to partial habitat overlap, extensive morphological similarity, and the lack of resolution when applying canonically reliable DNA barcoding approaches. In this study, we leveraged publicly available RAD-Seq data forL. campechanusandL. purpureusto identify species-informative single‐nucleotide polymorphisms (SNPs) at the genome scale that were successful in distinguishing the Northern and Southern red snappers, while also detecting individuals exhibiting introgression. This 4-step empirical approach demonstrates the value of applying novel bioinformatics pipelines to existing genome-scale data to maximize the distillation of informative subsets. Our results facilitate economically relevant species identification in addition to confirming or challenging species identifications for specimens with data in public databases. These findings and their applications will benefit future sustainability strategies and broader research questions surrounding these overfished and evolutionarily entangled snapper species.

Environmental Sciences & Ecology↗
DOE OSTI2021

Crystallization and Phase Transformations of Aluminum (Oxy)hydroxide Polymorphs in Caustic Aqueous Solution

Gibbsite, bayerite, and boehmite are important aluminum (oxy)hydroxide minerals in nature and have been widely deployed in various industrial applications. They are also major components in caustic nuclear wastes stored at various U.S. locations. Knowledge of their crystallization and phase transformation processes contributes to understanding their occurrence and could help optimize waste treatment processes. While it has been reported that partial conversion of bayerite and gibbsite to boehmite occurs in basic solutions at elevated temperatures, systematic studies of factors affecting the phase transformation as well as the underlying reaction mechanisms are non-existent, particularly in highly alkaline solutions. We explored the effects of sodium hydroxide concentrations (0.1~3 M), reaction temperature (60~100 ?) and aluminum concentrations (0.1~1 M) on the crystallization and transformation of these aluminum (oxy)hydroxides. Detailed structural and morphological characterization by X-ray diffraction (XRD), scanning electron microscopy (SEM), and nuclear magnetic resonance (NMR) spectrometry revealed that these processes depend largely on the reaction temperature and the Al/OH- ratio. When 1 = Al/OH- = 2.5, the reactions favor formation of high crystallinity precipitates, whereas at Al/OH- ratio ? 2.5 precipitation ceases unless the Al concentration is higher than 1 M. We identified pseudoboehmite, bayerite and gibbsite as intermediate phases to bayerite, gibbsite and boehmite, respectively, all of which transform via dissolution-reprecipitation. Gibbsite transforms to boehmite in both acidic and weak caustic environments at temperatures above 80 oC. However, a ‘bar-shaped’ gibbsite morphology dominates in highly caustic environments (3 M NaOH). The findings enable a robust basis for selection of various solid phases by tuning the reaction conditions.

aluminum (oxy)hydroxide polymorphs, crystallizatio↗
DOE OSTI2020

Crystallization of TiO 2 polymorphs from RF-sputtered, amorphous thin-film precursors

Crystalline TiO 2 films of anatase, brookite, and rutile are reproducibly made from amorphous precursors deposited by RF magnetron sputtering, producing large-area, single phase films of uniform thickness. Sputtered amorphous TiO 2 precursor thin films follow the general behavior observed for amorphous precursor thin films generated by pulsed laser deposition, namely, that oxygen deficiency is necessary for the formation of brookite and rutile. We quantify the oxygen deficiency and correlate it with the long wavelength optical absorption. We find that the precursor deposition rate is also a contributing factor to phase selection and that brookite and rutile form from films deposited more rapidly and anatase from films deposited more slowly. Sputtered and pulsed laser deposited amorphous precursor films prepared with similar oxygen deficiency and similar thickness result in the same final state after annealing, but the rate for sputtered precursors is slower.

14 SOLAR ENERGY↗
DOE OSTI2025

Formation of distinctive nanostructured metastable polymorphs mediated by kinetic transition pathways in germanium

High-pressure β -Sn germanium may transform into diverse metastable allotropes with distinctive nanostructures and unique physical properties via multiple pathways under decompression. However, the mechanism and transition kinetics remain poorly understood. Here, we investigate the formation of metastable phases and nanostructures in germanium via controllable transition pathways of β -Sn Ge under rapid decompression at different rates. High-resolution transmission electron microscopy reveals three distinct metastable phases with the distinctive nanostructures: an almost perfect st12 Ge crystal, nanosized bc8/r8 structures with amorphous boundaries, and amorphous Ge with nanosized clusters (0.8–2.5 nm). Fast in situ x-ray diffraction and x-ray absorption measurements indicate that these nanostructured products form in certain pressure regions via distinct kinetic pathways and are strongly correlated with nucleation rates and electronic transitions mediated by compression rate, temperature, and stress. This work provides deep insight into the controllable synthesis of metastable materials with unique crystal symmetries and nanostructures for potential applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Explainable Synthesizability Prediction of Inorganic Crystal Polymorphs Using Large Language Models

Abstract We evaluate the ability of machine learning to predict whether a hypothetical crystal structure can be synthesized and explain those predictions to scientists. Fine‐tuned large language models (LLMs) trained on a human‐readable text description of the target crystal structure perform comparably to previous bespoke convolutional graph neural network methods, but better prediction quality can be achieved by training a positive‐unlabeled learning model on a text‐embedding representation of the structure. An LLM‐based workflow can then be used to generate human‐readable explanations for the types of factors governing synthesizability, extract the underlying physical rules, and assess the veracity of those rules. These explanations can guide chemists in modifying or optimizing non‐synthesizable hypothetical structures to make them more feasible for materials design.

Kim, Seongmin [Department of Chemical and Biologic↗
DOE OSTI2025

Explainable Synthesizability Prediction of Inorganic Crystal Polymorphs Using Large Language Models

Abstract We evaluate the ability of machine learning to predict whether a hypothetical crystal structure can be synthesized and explain those predictions to scientists. Fine‐tuned large language models (LLMs) trained on a human‐readable text description of the target crystal structure perform comparably to previous bespoke convolutional graph neural network methods, but better prediction quality can be achieved by training a positive‐unlabeled learning model on a text‐embedding representation of the structure. An LLM‐based workflow can then be used to generate human‐readable explanations for the types of factors governing synthesizability, extract the underlying physical rules, and assess the veracity of those rules. These explanations can guide chemists in modifying or optimizing non‐synthesizable hypothetical structures to make them more feasible for materials design.

Kim, Seongmin [Department of Chemical and Biologic↗
DOE OSTI2023

Photocatalytic degradation of orange II dye via high pore volume polymorph zirconium-doped titania under visible light irradiation

A series of mixed-phase Zr-doped TiO 2 was utilized for the photocatalytic degradation of orange II dye. These materials were synthesized through a sol–gel technique by varying the amounts of zirconium in the photocatalysts. These materials were characterized using X-ray diffraction (XRD), transmission electron microscopy (TEM), X-ray fluorescence (XRF), Raman spectroscopy, thermogravimetry analysis (TGA), and X-ray photoelectron spectroscopy (XPS) among others. XRF and XPS data showed that the elemental composition of the photocatalysts consists of zirconium, titanium, and oxygen. In addition, XRD and Raman spectroscopy confirmed the existence of anatase and rutile phases of TiO 2 . The TGA analyses showed that the undoped TiO 2 was the most stable, with no significant weight loss during the heating range. Furthermore, the materials can effectively degrade orange II dye solution up to 7 cycles through asymmetric cleavage of the azo bond.

36 MATERIALS SCIENCE↗