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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Peripheral positions encode transport specificity in the small multidrug resistance exporters

In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.

Science & Technology - Other Topics↗
DOE OSTI2022

Laser-induced-fluorescence imaging of a spin-polarized ultracold neutral plasma in a magnetic field

In this work, we report Doppler-sensitive laser-induced-fluorescence (LIF) imaging of an ultracold neutral plasma in a magnetic field. Local values of ion density, hydrodynamic fluid velocity, temperature, and spin polarization are obtained using a fluorescence model based on velocity-resolved rate equations (REs) including the transfer of ions between states due to laser coupling and spontaneous emission. The RE approach captures optical pumping of ions into states that are not driven by the LIF excitation laser, and this is validated with experimental data. Combined molecular-dynamics and quantum-trajectories simulations verify that velocity-changing collisions have a negligible impact on the state population evolution for typical experimental conditions. Relative intensities of Zeeman components of the LIF spectra provide clear evidence that the ions are electron-spin-polarized when created by photoionization of magnetically trapped 88 Sr atoms. This probe opens many possibilities for studying thermal transport and the equilibration of neutral plasmas in overlapping regimes of strong coupling and magnetization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Phenomenology of Intermediate Molecular Dynamics at Metal-Oxide Interfaces

Reaction intermediates buried within a solid-liquid interface are difficult targets for physiochemical measurements. They are inherently molecular and locally dynamic, while their surroundings are extended by a periodic lattice on one side and the solvent dielectric on the other. Challenges compound on a metal-oxide surface of varied sites and especially so at its aqueous interface of many prominent reactions. Recently, phenomenological theory coupled with optical spectroscopy has become a more prominent tool for isolating the intermediates and their molecular dynamics. The following article reviews three examples of the SrTiO3-aqueous interface subject to the oxygen evolution from water: reaction-dependent component analyses of time-resolved intermediates, a Fano resonance of a mode at the metal-oxide–water interface, and reaction isotherms of metastable intermediates. The phenomenology uses parameters to encase what is unknown at a microscopic level to then circumscribe the clear and macroscopically tuned trends seen in the spectroscopic data.

Chemistry↗
DOE OSTI2023

Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site

Background: Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production. Results: Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H 2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains. Conclusion: The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O 2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Analysis of scintillation light dependence on liquid Argon purity

Previous studies have investigated the correlation between impurity concentrations in Liquid Argon (LAr) and the temporal evolution of either the slow scintillation decay time or the light yield. These impurities typically consist of various molecular species. Electronegative contaminants directly affect electron drift and photon production, while other molecules, such as nitrogen (N_2),can influence LAr scintillation properties without necessarily affecting electron lifetime. Many current and future neutrino and dark-matter experiments use LAr detectors. This study aims to evaluate the measured electron lifetimes in relation to the timing characteristics of the scintillation light signal in the SBN ICARUS detector at Fermi National Accelerator Laboratory. The ICARUS experiment consists of two cryostats that have shown some discrepancies in the measured electron lifetime over the years. In particular, this study addresses the use of data collected under varying purity conditions in the two cryostats.

Saia, Clara [Catania Astrophys. Observ.]↗
DOE OSTI2025

Developing reliable machine learning interatomic potential for Fe–Cr–Ni austenitic alloys

Gaining atomistic understanding of mechanical behavior of heat-resistant structural materials such as Fe–Cr–Ni-based alloys requires an approach with an accuracy close to density functional theory (DFT) that considers the intrinsic properties of the bulk lattice and important defects such as stacking faults, grain boundaries, and surfaces. This work aims to develop reliable machine learning interatomic potential (MLIAP) at cross-scale for Fe–Cr–Ni ternary alloys with a focus on the face-centered-cubic (fcc) solid solution structure. Leveraging the advantages of moment tensor potentials, which typically necessitate a relatively small training dataset and enable rapid calculations using the large-scale atomic/molecular massively parallel simulator package, we ensure the stability and accuracy of the trained potentials. Important defects such as stacking faults, grain boundaries, and surfaces for wide-range compositions are investigated. Structural, thermal, elastic, and defect properties are determined from molecular dynamics simulations comprising several thousand atoms, generated via canonical Monte Carlo simulations guided by the trained potential. The trained potential allows efficient atomic simulations of structural, thermal, and mechanical properties of fcc Fe–Cr–Ni solid solution alloys as a function of composition and temperature. Therefore, the MLIAP approach represents a major advancement from DFT calculations that are limited to small simulation sizes and traditional molecular dynamics simulations using relatively low accuracy potentials. Furthermore, this work outlines a practical foundation for further investigating the structural evolution and mechanical behavior of austenitic stainless steel and nickel-based alloys in a wide array of applications in extreme environments.

Crystal structure↗
DOE OSTI2021

The Galactic Chemical Evolution of Chlorine

We measured {sup 35}Cl abundances in 52 M giants with metallicities in the range −0.5 < [Fe/H] < 0.12. Abundances and atmospheric parameters were derived using infrared spectra from CSHELL on the NASA Infrared Telescope Facility and from optical echelle spectra. We measured Cl abundances by fitting a H{sup 35}Cl molecular feature at 3.6985 μm with synthetic spectra. We also measured the abundances of O, Ca, Ti, and Fe using atomic absorption lines. We find that the [Cl/Fe] ratio for our stars agrees with chemical evolution models of Cl, and the [Cl/Ca] ratio is broadly consistent with the solar ratio over our metallicity range. Both indicate that Cl is primarily made in core-collapse supernovae with some contributions from Type Ia supernovae. We suggest that other potential nucleosynthesis processes, such as the ν-process, are not significant producers of Cl. Finally, we also find our Cl abundances are consistent with H ii and planetary nebular abundances at a given oxygen abundance, although there is scatter in the data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Controlled Acidity Gradients Enable CO 2 Reduction to Formic Acid (Not Formate) by Molecular Electrocatalysts

Neutral or basic conditions are commonly required for the selective electrochemical reduction of CO 2 , leading to the accumulation of carbonate salts and the generation of formate rather than formic acid. A generalizable strategy for obtaining formic acid (not formate) in the electroreduction of CO 2 with molecular catalysts is introduced, based on controlling acidity gradients using a dual-electrolyte cell with a proton-exchange membrane. This approach uses anodic water oxidation as the source of protons and electrons for CO 2 reduction to formic acid, while mitigating H 2 evolution near the cathode and avoiding carbonate formation. Mechanistic studies, including systems modeling, provide insight into the origin of the formic acid selectivity and guide the broader implementation of this strategy in molecular electrocatalysis for CO 2 utilization.

Alcohols↗
DOE OSTI2024

Molecular Models of Atomically Dispersed Uranium at MoS 2 Surfaces Reveal Cooperative Mechanism of Water Reduction

Single atoms of uranium supported on molybdenum sulfide surfaces (U@MoS 2 ) have been recently demonstrated to facilitate the hydrogen evolution reaction (HER) through electrocatalysis. Theoretical calculations have predicted uranium hydroxide moieties bound to edge-sulfur atoms of MoS 2 as a proposed transition state involved in the HER process. However, the isolation of relevant intermediates involved in this process remains a challenge, rendering mechanistic hypotheses unverified. The present work describes the isolation and characterization of a uranium-hydroxide intermediate on molybdenum sulfide surfaces using [(Cp* 3 Mo 3 S 4 )UCp*], a molecular model of a reduced uranium center supported at MoS 2 . Mechanistic investigations highlight the metalloligand cooperativity with uranium involved in the water activation pathway. The corresponding uranium-oxo analogue, [(Cp* 3 Mo 3 S 4 )Cp*U(═O)], was also accessed from the hydroxide cluster via hydrogen atom transfer and from [(Cp* 3 Mo 3 S 4 )UCp*] through an alternative direct oxygen atom transfer. These results provide an atomistic perspective on the reactivity of low-valent uranium at molybdenum sulfide surfaces toward water, modeling key intermediates associated with the HER of U@MoS 2 catalysts.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Unraveling the electronic structure and magnetic transition evolution across monolayer, bilayer, and multilayer ferromagnetic Fe 3 GeTe 2

Two-dimensional (2D) van der Waals (vdW) magnets have sparked widespread attention due to their potential in spintronic applications as well as in fundamental physics. Ferromagnetic vdW compound Fe 3 GeTe 2 (FGT) and its Ga variants have garnered significant interest due to their itinerant magnetism, correlated states, and high magnetic transition temperature. Experimental studies have demonstrated the tunability of FGT’s Curie temperature, T C , through adjustments in quintuple layer numbers (QL) and carrier concentrations, n. However, the underlying mechanism remains elusive. In this study, we employ molecular beam epitaxy (MBE) to synthesize 2D FGT films down to 1 QL with precise layer control, facilitating an exploration of the band structure and the evolution of itinerant carrier density. Angle-resolved photoemission spectroscopy (ARPES) reveals significant band structure changes at the ultra-thin limit, while first-principles calculations elucidate the band evolution from 1 QL to bulk, largely governed by interlayer coupling. Additionally, we find that n is intrinsically linked to the number of QL and temperature, with a critical value triggering the magnetic phase transition. Our findings underscore the pivotal role of band structure and itinerant electrons in governing magnetic phase transitions in such 2D vdW magnetic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

NMR Studies of Block Copolymer-Based Supramolecules in Solution

Hierarchical assemblies from block copolymer (BCP)-based supramolecules have shown immense potential as programmable materials owing to their versatility for incorporating functional molecules and provide access to arrays of hierarchical structures. However, there remains a knowledge gap on the formation of the supramolecule in solution. Here, we applied NMR techniques to investigate the solution-phase behavior of the most studied supramolecular systems, polystyrene-block-poly(4-vinylpyridine)(3-pentadecylphenol) (PS-b-P4VP(PDP) r ). The results show that the supramolecule likely adopts a coil-comb conformation, despite the small molecule's (PDP) rapid exchange between the bonded and free states. The exchange rate (>10 4 s -1 ) exceeds the NMR time scale at the frequency of interest. The supramolecules form under dilute conditions (~2 vol %) and are attributed to the enthalpic gain of the hydrogen bonding between the PDP and 4VP. As the solute concentration increases (>10 vol %), the supramolecule forms micelle-like aggregates with PDP accumulated within the comb-block's pervaded volume based on analysis of the apparent molecular weight, viscosity, and chain dynamics. Overall, this work sheds light on the long-standing question regarding the evolution of the constituents in the BCP-based supramolecule in solution and provides valuable guidance toward their solution-based processing and morphological control.

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

Multiprincipal Component P2-Na 0.6 (Ti 0.2 Mn 0.2 Co 0.2 Ni 0.2 Ru 0.2 )O 2 as a High-Rate Cathode for Sodium-Ion Batteries

Mixing transition metal cations in nearly equiatomic proportions in layered oxide cathode materials is a new strategy for improving the performances of Na-ion batteries. The mixing of cations not only offers entropic stabilization of the crystal structure but also benefits the diffusion of Na ions with tuned diffusion activation energy barriers. In light of this strategy, a high-rate Na 0.6 (Ti 0.2 Mn 0.2 Co 0.2 Ni 0.2 Ru 0.2 )O 2 cathode was designed, synthesized, and investigated, combining graph-based deep learning calculations and complementary experimental characterizations. This new cathode material delivers high discharge capacities of 164 mA g –1 at 0.1 C and 68 mAh g –1 at a very high rate of 86 C, demonstrating an outstanding high rate capability. Ex situ and operando synchrotron X-ray diffraction were used to reveal the detailed structural evolution of the cathode upon cycling. Using the climbing-image nudged elastic-band calculation and Ab initio molecular dynamics simulations, we show that the optimal transition metal composition enables a percolating network of low barrier pathways for fast, macroscopic Na diffusion, resulting in the observed high rate performance.

25 ENERGY STORAGE↗
DOE OSTI2023

A Re-Evaluation of African Swine Fever Genotypes Based on p72 Sequences Reveals the Existence of Only Six Distinct p72 Groups

The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins

Single-strand RNA (ssRNA) Fiersviridae phages cause host lysis with a product of single gene (sgl for single-gene lysis; product Sgl) that induces autolysis. Many different Sgls have been discovered, but the molecular targets of only a few have been identified. In this study, we used a high-throughput genetic screen to uncover genome-wide host suppressors of diverse Sgls. In addition to validating known molecular mechanisms, we discovered that the Sgl of PP7, an ssRNA phage of Pseudomonas aeruginosa, targets MurJ, the flippase responsible for lipid II export, previously shown to be the target of the Sgl of coliphage M. These two Sgls, which are unrelated and predicted to have opposite membrane topology, thus represent a case of convergent evolution. We extended the genetic screens to other uncharacterized Sgls and uncovered a common set of multicopy suppressors, suggesting that these Sgls act by the same or similar mechanism.

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

Elasticity of two-dimensional ferroelectrics across their paraelectric phase transformation

The mechanical behavior of two-dimensional (2D) materials across 2D phase changes is unknown, and the finite temperature (T) elasticity of paradigmatic SnSe monolayers—ferroelectric 2D materials turning paraelectric as their unit cell turns from a rectangle into a square—is described here in a progressive manner. To begin with, their zero–T total energy landscape gives way to (Boltzmann-like) averages from which the elastic behavior is determined. Furthermore, these estimates are complemented with results from the strain-fluctuation method, which employs the energy landscape or ab initio molecular dynamics data. All approaches capture the coalescence of elastic moduli < C 11 (T) > = < C 22 (T) > due to the structural transformation. The broad evolution and sudden changes of elastic parameters < C 11 (T) >, < C 22 (T) >, and < C 12 (T) > of these atomically thin phase-change membranes establishes a heretofore overlooked connection among 2D materials and soft matter.

2-dimensional systems↗
DOE OSTI2020

Unraveling Spatio-Temporal Chemistry Evolution in Laser Ablation Plumes and Its Relation to Initial Plasma Conditions

The chemistry evolution in a laser ablation plume depends strongly on its initial physical conditions. In this article, we investigate the impact of plasma generation conditions on the interrelated phenomena of expansion dynamics, plasma chemistry, and physical conditions. Plasmas are produced from a uranium metal target in air using nanosecond, femtosecond, and femtosecond filament-assisted laser ablation. Time-resolved two-dimensional spectral imaging was performed for evaluating the spatio-temporal evolu-tion of atoms, diatoms, polyatomic molecules, and nanoparticles in situ. Emission spectral features reveal that molecular formation occurs at early times in both femtosecond and filament ablation plumes, although with different temporal decay. In contrast, mo-lecular formation is found to occur at much later times in nanosecond plasma evolution. Spectral modeling is used to infer tem-poral behavior of plasma excitation temperature, and results highlighted that nanosecond plume temperatures decay rapidly while plumes generated by filament ablation show slowest decay. In this work, we find U atoms and UO molecules co-exist in ultrafast laser produced plasmas even at early times after plasma onset owing to favorable temperatures for molecular formation. Regardless of irradiation conditions, plume emission features showed presence of higher oxides (i.e. UxOy), although with different temporal histories. Our study provides insight into the impact of plasma generation conditions on chemistry evolution in plasmas produced from traditional focused femtosecond, nanosecond, and filament-assisted laser ablation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗