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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Effect of iron redox ratio on the structures of boroaluminosilicate glasses

Iron oxide is commonly found in natural or industrial glass compositions and can exist as ferrous (Fe 2+ ) or ferric (Fe 3+ ) species, with their ratios depending on glass composition, temperature, pressure and the redox reactions during the glass forming process. The iron redox ratio plays an important role on silicate glass structures and consequently various properties. This work aims to study the effect of iron oxide, and particularly the iron redox ratio, on the structures of borosilicate and boroaluminosilicate glasses using molecular dynamics simulations with newly developed iron potential parameters that are compatible with the borosilicate potentials. The results provide detailed cation coordination states of both iron species and the effect of redox ratio on boron coordination and other structural features. Particularly, competition for charge compensating modifier cations (such as Na + ) among the fourfold-coordinated cations such as B 3+ , Al 3+ , and Fe 3+ is investigated by calculating the cation–cation pair distribution functions and coordination preferential ratios. The results show that the trivalent ferric ions, with a shorter Fe–O bond distance and better defined first coordiation shell with mainly four-fold coordination, act as a glass former whereas the divalent ferrous ions mainly play the role of glass modifier. The ferrous/ferric ratio (Fe 2+ /Fe 3+ ) was found to affect the glass chemistry and hence glass properties by regulating the amount of four-coordinated boron, the fraction of non-briding oxygen and other features. Finally, the results are compared with available experimental data to gain insights of the complex structures and charge compensation schemes of the glass system.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Surface and bulk characterization of reservoir and cap-rocks: Past, present, and future

Geologic formations provide potentially some of the largest volume capacities for CO 2 storage or sequestration. Potential storage sites can be deep saline aquifers, depleted oil reservoirs, and coal seams, surrounded by sealing layers to prevent CO 2 from leaking. It is therefore critical to understand mechanisms contributing to CO 2 trapping and CO 2 leaks. Both phenomena are governed by reactions at the interfaces of the reservoir and cap-rocks and are controlled by the complex chemistry and pore structures of rocks. Mechanisms at the macroscale are affected by the processes occurring at the nanoscale. This review highlights the necessity of multitechnique, multiscale characterization of rocks and points to the importance of surface analysis and surface science studies. Two shale rocks (seals) from Niobrara and Agardhfjellet formations with complex surface chemistry are used as examples throughout the paper. Typically, evaluation of rocks with x-ray diffraction, thermogravimetric analysis, Rock-Eval pyrolysis, gas adsorption, and electron microscopy combined with energy dispersive x-ray spectroscopy is conducted to provide valuable information about the bulk mineralogy, elemental composition, pore volume, and adsorbed species on the sample surface. These studies are necessary prior to designing surface sensitive experiments with x-ray photoelectron spectroscopy (XPS), guiding both sample preparation and sample analysis. XPS has been widely used to study the surface composition of rocks during the investigations of their fine-scale wettability, and the main findings are highlighted here. This paper also reviews the existing literature on ambient-pressure XPS, which provides new opportunities to study in situ chemical alteration due to interactions with CO 2 and offers recommendations for adapting this technique to study rock-fluid interactions, allowing for the identification of fundamental interactions during CO 2 sequestration and guide selection of formation sites for improved storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Ab initio molecular dynamics (AIMD) simulations of NaCl, UCl 3 molten salts

Ab initio molecular dynamics (AIMD) simulations are used to calculate select thermophysical and thermodynamic properties of NaCl, UCl and NaCl-UCl 3 molten salts. Following established approaches, the AIMD simulations include a model for Van der Waals interactions. The Langreth & Lundqvist (vDW-DF2), DFT-D3, and density-dependent energy correction (DFT-dDsC) dispersion models are first tested for molten NaCl in order to assess their accuracy for density and heat capacity predictions across a range of temperatures. Based on the NaCl results, the vdW-DF2 and DFT-dDsC methods are extended to the UCl 3 system and compared to available experimental data. Next, mixtures of NaCl-UCl 3 are investigated and analyzed with respect to the deviation from ideal solution behavior. For the DFT-dDsC simulations, density deviates by up to 2% from an ideal mixture, with the maximum occurring close to the eutectic composition. The mixing energy also deviates from an ideal solution and exhibits a minimum of about -0.074 to eV per formula unit, again close to the eutectic composition. Finally, the compressibility and species diffusivity of the pure and mixed salt systems are calculated. The diffusivities are slightly reduced in the mixed compared to the pure systems and the compressibilities loosely follow a linear correlation as a function of the UCl 3 composition. The trends observed for mixing properties are rationalized by correlating them to the coordination chemistry, which emphasizes the importance of maintaining the extended network formed by U and Cl ions as the NaCl concentration increases. The concentration at which breakdown of the extended network occurs, roughly coincides with the minimum of both the mixing energy and the deviation from ideal solution behavior for density.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Comparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomass

Abstract Background Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals. Results The authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed. Conclusions This work demonstrates that different methods using chemical, thermal, and non-destructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.

09 BIOMASS FUELS↗
DOE OSTI2025

Delineating the Effects of Counterions on the Structural and Vibrational Properties of U(IV) Lindqvist Polyoxometalate Complexes

Herein we conducted a full investigation into the fundamental structural and vibrational properties of uranium(IV) Peacock−Weakley-type lacunary Lindqvist (W 10 ) polyoxometalate (POM) complexes. We recently demonstrated the importance of the secondary lattice elements in tuning the distortion of the D 4d symmetry in W 10 POM complexes, and here, we synthesized eight UW 10 complexes with different alkali metal counterions and evaluated how the composition and packing of counterion species affected complex structural and vibrational properties. Single-crystal X-ray diffraction analysis on complexes 1−8 revealed changes in structural distortion parameters as a function of differences in counterion configurations, while far-infrared and Raman spectra for 1−8 also demonstrated that vibrational mode frequencies were sensitive to changes in counterion composition and packing. To more effectively compare different counterion configurations, we developed counterion effective ionic radius (eIR) as a new structural parameter, and comparisons between structural distortion parameters and eIR values strongly suggested that modulation by the secondary lattice elements can affect structural and vibrational manifolds within POM complexes. Partial least squares (PLS) analysis was used to quantitatively evaluate correlations observed within this investigation, and PLS statistical models showed a strong correlation between counterion eIR and both structural distortion parameters and vibrational mode frequencies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Chemical identification of new particle formation and growth precursors through positive matrix factorization of ambient ion measurements

Abstract. In the lower troposphere, rapid collisions between ions and trace gases result in the transfer of positive charge to the highest proton affinity species and negative charge to the lowest proton affinity species. Measurements of the chemical composition of ambient ions thus provide direct insight into the most acidic and basic trace gases and their ion–molecule clusters – compounds thought to be important for new particle formation and growth. We deployed an atmospheric pressure interface time-of-flight mass spectrometer (APi-ToF) to measure ambient ion chemical composition during the 2016 Holistic Interactions of Shallow Clouds, Aerosols, and Land Ecosystems (HI-SCALE) campaign at the United States Department of Energy Atmospheric Radiation Measurement facility in the Southern Great Plains (SGP), an agricultural region. Cations and anions were measured for alternating periods of ∼ 24 h over 1 month. We use binned positive matrix factorization (binPMF) and generalized Kendrick analysis (GKA) to obtain information about the chemical formulas and temporal variation in ionic composition without the need for averaging over a long timescale or a priori high-resolution peak fitting. Negative ions consist of strong acids including sulfuric and nitric acid, organosulfates, and clusters of NO3- with highly oxygenated organic molecules (HOMs) derived from monoterpene (MT) and sesquiterpene (SQT) oxidation. Organonitrates derived from SQTs account for most of the HOM signal. Combined with the diel profiles and back trajectory analysis, these results suggest that NO3 radical chemistry is active at this site. SQT oxidation products likely contribute to particle growth at the SGP site. The positive ions consist of bases including alkyl pyridines and amines and a series of high-mass species. Nearly all the positive ions contained only one nitrogen atom and in general support ammonia and amines as being the dominant bases that could participate in new particle formation. Overall, this work demonstrates how APi-ToF measurements combined with binPMF analysis can provide insight into the temporal evolution of compounds important for new particle formation and growth.

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

Z-Contrast Enhancement in Au–Pt Nanocatalysts by Correlative X-ray Absorption Spectroscopy and Electron Microscopy: Implications for Composition Determination

The properties of bimetallic nanoparticles (BNPs) vary widely as a function of their composition and size distributions. X-ray absorption fine structure analysis is commonly used to characterize their structure, but its application to elements that are close to each other in the periodic table is hampered by poor Z-contrast. For this study, we trained an artificial neural network to recognize the partial coordination numbers in AuPt NPs synthesized via peptide templating using their X-ray absorption near-edge structure spectra. This approach, combined with scanning transmission electron microscopy analysis, revealed unique details of this prototype catalytic system that has different forms of heterogeneities at both the intra- and inter-particle levels. Our method based on the enhancement of Z-contrast of metal species will have implications for compositional studies of BNPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Secondary Organic Aerosol from OH Oxidation of Acyclic Terpenes Is More Viscous and Less Volatile than That of Their Cyclic Analogs

Biogenic volatile organic compounds (BVOCs), a dominant source of secondary organic aerosol (SOA) globally, exhibit emission rates and composition that are plant species-specific and vary with environmental stressors. A common outcome of plant stress is increased emissions of acyclic terpenes. The paucity of information about acyclic terpene SOA chemistry contributes to uncertainties in predictions of SOA global loadings and impacts on Earth’s radiative budget, particularly in a changing climate where acyclic terpene emissions could become more prominent. This study compared properties of SOA derived from OH oxidation of acyclic and cyclic monoterpenes (ß-ocimene, a-pinene) and sesquiterpenes (ß-farnesene, ß-caryophyllene). Single particle mass spectrometry was used for assessing shape, density, and evaporation kinetics of size-selected SOA particles, and nanospray desorption electrospray ionization high-resolution mass spectrometry (nano-DESI-HRMS) was used to measure molecular composition of SOA. Acyclic terpene SOA exhibited higher viscosity and lower volatility compared to cyclic terpene SOA, and had a greater volume fraction remaining (VFR) after ~24 hours of evaporation - approximately 1.3-1.6 times higher VFR than that of cyclic terpene SOA. Additionally, HRMS analysis revealed greater chemical diversity and higher fractions of extremely low volatility compounds (56-62% ELVOC/LVOC) in acyclic terpene SOA compared to cyclic counterparts (25-37% ELVOC/LVOC). Our findings highlight the potential importance of accounting for acyclic terpene aerosol chemistry under conditions of plant stress to improve predictions of SOA loadings and impacts.

SOA physical properties↗
DOE OSTI2024

Investigation of Frozen Chemistry for Molten Salt Reactors (MSRs)

Understanding accident progression and the potential/conditions for fission product release from fuel is necessary to evaluate safety for any nuclear reactor system. Molten Salt Reactors (MSRs) under development need such analysis to support safety evaluations. Fission product chemistry specific to MSR concepts is a critical area that introduces distinct considerations relative to the current state-of-knowledge in reactor safety, primarily developed for water-moderated nuclear reactor systems. In Light Water Reactor (LWR) systems, it is necessary to capture the chemical interaction of fission products with the reactor evironment, containment and confinement systems. The overall effects at this point are relatively well understood for the purposes of performing safety evaluations. A key insight from LWR studies is that fission product chemical behavior can be reasonably captured by modeling approaches where the chemistry is "frozen". These modeling approaches assume that radionuclide reaction and speciation can be represented by chemical classes, each with characteristic transport behavior that is invariant under a broad range of thermochemical conditions. However, radionuclides can exhibit a range of behavior in the liquid salt-melt phase of the coolant used in MSRs. Radionuclides, salt, and the metal containment surfaces (i.e. pipes) can co-exist in dynamic equilibrium that could evolve with small system mass changes. A detailed investigation to the degree the equilibrium state can dynamically evolve with changes in the conditions of the molten salt mixture has not been previously conducted. It is currently not well understood where frozen chemistry assumptions are valid. Expanding the state-of-knowledge in this regard is relevant to better assessing the range of chemical effects that should be incorporated as part of MSR safety assessments. This investigation used the Oak Ridge Isotope GENeration (ORIGEN) module of the Standardized Computer-Analysis for Licensing Evaluation (SCALE) code to generate simulated radionuclide inventories for the MSR Experiment (MSRE) and then modeled reactor chemical speciation using the Molten Salt Thermodynamic Database – Thermochemical (MSTDB-TC) coupled with Thermochimica. The effect of composition variation during decay of fission product inventory in a molten salt over a period of 500 days prolonged post- at multiple temperatures was studied. Mass fractions for fluorine and berilium were varied in order to probe the effects of free fluorine control. Finally, speciation of fluoride reactors were showed by comparing MSRE readionuclide inventories with a FLiBe based molten salt breeder reactor (MSBR). The results showed that fission product mass change has little effect on phase mass changes and vapor pressures for fluoride species, but differ with varying carrier and fuel salt compositions. However, iodine species were found to have a vapor pressure not only dependent on temperature, but also the free fluorine potential, releasing iodine when the free fluorine potential is equal to the iodine inventory. This observation, however, arose under free fluorine potentials that are very unlikely to be realized in typical molten salt mixtures. Despite this observation, temperature was found to be the dominant parameter that drove phase change and fission product species vapor pressure. The results indicate that the current frozen chemistry approach is adequate for MSR analysis.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Active Thermochemical Tables: Enthalpies of Formation of Bromo- and Iodo-Methanes, Ethenes and Ethynes

Here, the thermochemistry of halocarbon species containing iodine and bromine is examined through an extensive interplay between new Feller–Peterson–Dixon (FPD) style composite methods and a detailed analysis of all available experimental and theoretical determinations using the thermochemical network that underlies the Active Thermochemical Tables (ATcT). From the computational viewpoint, a slower convergence of the components of composite thermochemistry methods is observed relative to species that solely contain first row elements, leading to a higher computational expense for achieving comparable levels of accuracy. Potential systematic sources of computational uncertainty are investigated, and, not surprisingly, spin-orbit coupling is found to be a critical component, particularly for iodine containing molecular species. The ATcT analysis of available experimental and theoretical determinations indicates that prior theoretical determinations have significantly larger uncertainties than originally reported, particularly in cases where molecular spin-orbit effects were ignored. Accurate and reliable heats of formation are reported for 38 halogen containing systems, based on combining the current computations with previous experimental and theoretical work via the ATcT approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota

The gut is continuously invaded by diverse bacteria from the diet and the environment, yet microbiome composition is relatively stable over time for host species ranging from mammals to insects, suggesting host-specific factors may selectively maintain key species of bacteria. To investigate host specificity, we used gnotobiotic Drosophila, microbial pulse-chase protocols, and microscopy to investigate the stability of different strains of bacteria in the fly gut. We show that a host-constructed physical niche in the foregut selectively binds bacteria with strain-level specificity, stabilizing their colonization. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus species physically remodels the niche through production of a glycan-rich secretion to favor secondary colonization by unrelated commensals in the Acetobacter genus. Our results provide a mechanistic framework for understanding the establishment and stability of a multi-species intestinal microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bridging Aromatic/Antiaromatic Units: Recent Advances in Aromaticity and Antiaromaticity in Main-group and Transition-Metal Clusters from Bonding and Magnetic Analyses

Synthetic exploration and theoretical characterization of metal clusters are actively developing branches of modern inorganic chemistry. Advances in these areas constantly expand the rich structural diversity of viable species, allowing a detailed study of the fundamental characteristics of bench-stable compounds. In this minireview, we summarize recent achievements in synthesis and computational analyses of main-group and heterometallic clusters containing multiple aromatic/antiaromatic units. These systems range from bare clusters to ligand-decorated aggregates, providing a fundamental understanding of the aromaticity and antiaromaticity concepts in species exhibiting unprecedented shapes and composition. The review gives a comprehensive summary of bonding and magnetic response properties of such systems deciphered from the Adaptive Natural Density Partitioning (AdNDP) approach and induced magnetic field analyses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Dredged sediments contain potentially beneficial microorganisms for agriculture and little harmful cyanobacteria

Soils worldwide are degrading, raising concerns about our ability to feed the growing global population. Soil amendments that can alleviate degradation are gaining attention. The application of sediments dredged from waterways to agricultural fields has increasing promise as a means for improving degraded soils. However, herbaceous plant species may have difficulty establishing on dredged material because of low nutrient availability, inhibitory levels of toxins, unsuitable moisture conditions and lack of microorganisms capable of ameliorating these characteristics. To counteract these issues, we sought to understand if the use of a cover crop would increase the abundance, diversity and function of beneficial soil microorganisms compared to harmful microorganisms in dredged sediments. We collected soil samples from two 100% dredged sediment plots, one where winter cereal rye (Secale cereal) was grown as a winter cover crop and one left fallow over the winter, followed by traditional corn (Zea mays) planting. We sampled both plots three times during the growing season: before cover crop application, following cover crop application but before corn planting and following final corn harvest. We then used high-throughput sequencing to identify the bacterial and fungal communities present in the samples. Our data show that cover crop application did not alter the microbial community in these plots. However, sampling time decreased species diversity and altered the composition of both fungal and bacterial communities recovered from these plots. Across both plots, microorganisms associated with carbon cycling were more abundant than those associated with harmful effects, including microcystin-producing cyanobacteria, which were an extremely small portion of the overall community. Our work suggests that dredged sediments have the potential to improve soil function through the addition of microorganisms associated with nutrient cycling, but a cover crop is not necessary to incur these benefits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Chemical and isotopic evolution of flowback fluids from the Utica Gas Shale Play, Eastern Ohio USA

For this work, hydraulic fracturing flowback fluids were collected from two Utica/Point Pleasant well pads in eastern Ohio. One site was in the wet gas zone (UPPW), while the site ~50 km south consisted of four wells on the same pad in the dry gas zone (UPPS). Samples of input fluids also were collected before and during hydraulic fracturing. Flowback fluids are Na-Ca-Cl brines with total dissolved salt (TDS) concentrations that increase over several months from ~100 to 200 g/L. The slightly higher TDS of the dry gas fluids are in part due to recycled flowback used as input fluids, and in part due to lower volume of water used in hydraulic fracturing. Concentrations of most major ions (Ca 2+ , Mg 2+ , Na + , Sr2 + , Fe, Mn, Cl – , Br – ) are similar for the five wells sampled, although small but systematic changes occur in the major element ratios over time. Most notably, an increase in the Sr/Cl ratio corresponds to an increase in the 87 Sr/ 86 Sr ratio in the fluids, suggesting interactions with a more radiogenic Sr source in the subsurface. Dissolved Ba concentrations and Ra activities were different between the two sites, reflecting a high SO 4 2– fluid used at the UPPW site, and water-rock reactions occurring during hydraulic fracturing at the UPPS site. Water oxygen (δ 18 O) and hydrogen (δD) isotopes for input fluids used in the UPPW4 well and fresh water used for the UPPS wells fall on the Global Meteoric waterline (GMWL). Flowback fluids from both sites are relatively enriched in δ 18 O and δD compared to the input, but do not appear to follow a simple mixing trend, suggesting reaction and isotopic exchange with carbonates and fractionation due to imbibition in the rock. Cl isotopes, δ 37 Cl in the FP fluids varied from ~ –0.43 to +0.13‰, the largest variation was observed in the earlier stages of flowback, while in the later stages δ 37 Cl exhibited a small but systematic increase over time, suggesting diffusion control of isotopic composition. Some of the trace species measured (dissolved Fe, Mn, thiosulfate and organic acids) do not follow the same trends as the major ions, suggesting contributions from input fluids, or microbially mediated reactions are exerting control on their concentrations. Input water chemistry exerts an important control on the Sr and Ba concentrations in flowback water. High SO 4 2– in the input fluids used for hydraulically fracturing the wet gas well leads to precipitation of barite-celestite in flowback fluids.

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

Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA

Abstract Saline springs within the Illinois Basin result from the discharge of deep‐seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%–94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Dynamics of plasma atomic layer etching: Molecular dynamics simulations and optical emission spectroscopy

Atomic layer etching is intrinsically dynamic as it involves sequential and repeated exposures of a surface to be etched with different species at different energies. The composition and structure of the near surface region change in both time and depth. Full understanding of this process requires resolving both temporal and spatial variations. In this work, we consider silicon (Si) atomic layer etching (ALE) by alternating exposure to chlorine gas (Cl 2 ) and argon ions (Ar + ). Molecular dynamics (MD) simulations are compared to experimental measurements with the aim of better understanding the dynamics of ALE and to test the simulation procedure. The simulations help to more fully interpret the experimental measurements. Further, optical emission measured just above the surface being etched can be related to etch products and can, therefore, be directly compared to simulation predictions. The simulations capture the measured initial product distribution leaving the surface and match the measured etch per cycle reasonably well. While simulations demonstrate the importance of ion-induced surface damage and mixing into a layer below the surface, the depth of which depends mainly on ion energy, the experiments suggest there is more Cl mixed into the layer than the MD procedure predicts.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome

Culture-independent characterization of microbial communities associated with popular plant model systems have increased our understanding of the plant microbiome. However, the integration of other model systems, such as duckweed, could facilitate our understanding of plant microbiota assembly and evolution. Duckweeds are floating aquatic plants with many characteristics, including small size and reduced plant architecture, that suggest their use as a facile model system for plant microbiome studies. Here, we investigated the structure and assembly of the duckweed bacterial microbiome. First, a culture-independent survey of the duckweed bacterial microbiome from different locations in New Jersey revealed similar phylogenetic profiles. These studies showed that Proteobacteria is a dominant phylum in the duckweed bacterial microbiome. To observe the assembly dynamics of the duckweed bacterial community, we inoculated quasi-gnotobiotic duckweed with wastewater effluent from a municipal wastewater treatment plant. Our results revealed that duckweed strongly shapes its bacterial microbiome and forms distinct associations with bacterial community members from the initial inoculum. Additionally, these inoculation studies showed the bacterial communities of different duckweed species were similar in taxa composition and abundance. Analysis across the different duckweed bacterial communities collected in this study identified a set of “core” bacterial taxa consistently present on duckweed irrespective of the locale and context. Furthermore, comparison of the duckweed bacterial community to that of rice and Arabidopsis revealed a conserved taxonomic structure between the duckweed microbiome and the terrestrial leaf microbiome. Our results suggest that duckweeds utilize similar bacterial community assembly principles as those found in terrestrial plants and indicate a highly conserved structuring effect of leaf tissue on the plant microbiome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗