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At least 1,297 records · Page 72

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO 2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO 2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

bacterial metabolism↗

Dispersion of high oxygen permeability ionomers in water-propanol solutions

There is a growing interest in high oxygen permeability ionomers (HOPI) for better-performing proton exchange membrane fuel cell (PEMFC) catalyst layers. In this study, we used small-angle x-ray scattering (SAXS) to analyze dispersions of two types of perfluorinated sulfonic acid (PFSA) ionomers and a HOPI in water and propanol solvents, at concentrations between 1 wt% and 15 wt%. HOPI dispersions exhibited the interference peak typical of ionomers; by separately fitting the peak and higher- q regions with several models, we demonstrated that HOPI aggregates have a closer average spacing than conventional PFSA ionomers, and smaller aggregate size when assuming a cylindrical geometry. By measuring conventional PFSA ionomers with two side chain lengths and several equivalent weights, we showed that these side chain parameters alone did not explain the differences in aggregate spacing or size. In addition, the pattern was present whether samples were prepared in a 50/50 water/propanol or a more propanol-rich mixture. As such, the structural differences of HOPI could be due to its different backbone monomer. A better understanding of the influence of the HOPI chemistry on dispersion properties could help explain the ink structure and drying characteristics of HOPI observed in prior work. Future study of ionomer-catalyst mixtures, such as measuring ionomer adsorption to carbon, would help elucidate the role of ionomer from ink formulation to the cast electrode.

Aquivion↗

The Virtual Environment for Reactor Applications (VERA): Design and architecture

VERA, the Virtual Environment for Reactor Applications, is the system of physics capabilities being developed and deployed by the Consortium for Advanced Simulation of Light Water Reactors (CASL). CASL was established for the modeling and simulation of commercial nuclear reactors. VERA consists of integrating and interfacing software together with a suite of physics components adapted and/or refactored to simulate relevant physical phenomena in a coupled manner. VERA also includes the software development environment and computational infrastructure needed for these components to be effectively used. We describe the architecture of VERA from both software and numerical perspectives, along with the goals and constraints that drove major design decisions, and their implications. We explain why VERA is an environment rather than a framework or toolkit, why these distinctions are relevant (particularly for coupled physics applications), and provide an overview of results that demonstrate the use of VERA tools for a variety of challenging applications within the nuclear industry.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Measurement and thermal modeling of sapphire substrate temperature at III-Nitride MOVPE conditions

Here, growth rates and alloy composition of AlGaN grown by MOVPE is often very temperature dependent due to the presence of gas-phase parasitic chemical processes. These processes make wafer temperature measurement highly important, but in fact such measurements are very difficult because of substrate transparency in the near- IR (~900 nm) where conventional pyrometers detect radiation. The transparency problem can be solved by using a mid-IR pyrometer operating at a wavelength (~7500 nm) where sapphire is opaque. We employ a mid- IR pyrometer to measure the sapphire wafer temperature and simultaneously a near-IR pyrometer to measure wafer pocket temperature, while varying reactor pressure in both a N 2 and H 2 ambient. Near 1300 °C, as the reactor pressure is lowered from 300 Torr to 10 Torr the wafer temperature drops dramatically, and the ΔT between the pocket and wafer increases from ~20 °C to ~250 °C. Without the mid-IR pyrometer the large wafer temperature change with pressure would not have been noted. In order to explain this behavior we have developed a quasi-2D thermal model that includes a proper accounting of the pressure-dependent thermal contact resistance, and also accounts for sapphire optical transmission. The model and experimental results demonstrate that at most growth conditions the majority of the heat is transported from the wafer pocket to the wafer via gas conduction, in the free molecular flow limit. In this limit gas conductivity is independent of gap size but first order in pressure, and can quantitatively explain results from 20 to 300 Torr. Further analysis yields a measure of the thermal accommodation coefficients; α(H 2 ) =0.23, α(N 2 ) =0.50, which are in the range typically measured.

36 MATERIALS SCIENCE↗

Computational modeling and neutron imaging to understand interface shape and solute segregation during the vertical gradient freeze growth of BaBrCl:Eu

In this work we apply continuum models to analyze phase change, heat transfer, fluid flow, solute transport, and segregation in order to understand prior neutron imaging observations of the vertical gradient freeze growth of Eu-doped BaBrCl. The models provide a rigorous framework in which to understand the mechanisms that are responsible for the complicated evolution of interface shape and dopant distribution in the growth experiment. We explain how a transition in the solid/liquid interface shape from concave to convex is driven by changes in radial heat transfer caused by furnace design. We also provide a mechanistic explanation of how dynamic growth conditions and changes of the flow structure in the melt result in complicated segregation patterns in this system. A growth pause caused by controller lock-up is shown to result in a band of solute depletion in accordance with classical theory. However, changing flow patterns during growth result in a non-monotonic axial distribution of solute that cannot be explained by simple application of classical segregation models. We assert that the approach presented here, namely the use of rigorous models in conjunction advanced diagnostics, such as neutron imaging, provides an exciting path forward for process optimization and control, accelerating the incremental advances that have, in the past, typically relied on empiricism, experience, and intuition.

36 MATERIALS SCIENCE↗

Spatial and temporal variability of tritium in precipitation within South Africa and it's bearing on hydrological studies

Tritium, the radioactive isotope of hydrogen, has been used to understand groundwater recharge processes for decades. The current variation of tritium in the atmosphere is largely attributed to stratospheric production and fall out rates as well as global circulation phenomena controlling the hydrological cycle. Global controls on the variability in atmospheric tritium activity are poorly suited to explain local variation and tritium activities in precipitation are often assumed to be uniform over both local and regional catchments and watersheds. This assumption can result in both over and under estimation of modern recharge within an aquifer when using tritium as the recharge proxy. In order to minimize the inherent prediction residuals associated with tritium based recharge investigations, the variability of tritium in precipitation was modelled from 127 spatial precipitation samples taken over a two year period, combined with a 76 precipitation sample group-set taken over a one year period in a single location. Precipitation events were traced backward in time, from the point of collection, using HYSPLIT modelling to ascertain the origins of moisture content as well as the altitudes of moisture origin reached along the particle track. Tritium activities, collected over a one year period in Paarl, range from 0.45 to 4.16 TU and have a mean of 1.59 TU. Spatial storm events in the Western Cape in 2017 and 2018 had a range from 0 to 2.2 and 0.37 to 3.27 TU, respectively, with mean activities of 1.18 (n = 34) and 1.25 TU (n = 32). Both storm events had similar tritium variability (σ = 0.5 n = 35 and 0.48 n = 32). Regional precipitation events had the largest range of tritium activities (0.55–12.2 TU). Although not all tritium activities can be explained by interrogating the water mass origin, this study suggests that approximately 90% of events can be completely or partially attributed to the origin of the water mass. The variability of tritium, both spatially and temporally, was higher than expected, confirming that when uniform tritium inputs are used, the groundwater system would provide inaccurate modern recharge estimates. Higher spatial resolution of tritium variation in precipitation for a particular region will improve our ability to relate tritium activities in groundwater to local precipitation.

54 ENVIRONMENTAL SCIENCES↗

Cosmology intertwined: A review of the particle physics, astrophysics, and cosmology associated with the cosmological tensions and anomalies

The standard Λ Cold Dark Matter (ΛCDM) cosmological model provides a good description of a wide range of astrophysical and cosmological data. However, there are a few big open questions that make the standard model look like an approximation to a more realistic scenario yet to be found. In this paper, we list a few important goals that need to be addressed in the next decade, taking into account the current discordances between the different cosmological probes, such as the disagreement in the value of the Hubble constant H 0 , the σ 8 – S 8 tension, and other less statistically significant anomalies. While these discordances can still be in part the result of systematic errors, their persistence after several years of accurate analysis strongly hints at cracks in the standard cosmological scenario and the necessity for new physics or generalisations beyond the standard model. In this paper, we focus on the 5.0 σ tension between the Planck CMB estimate of the Hubble constant H 0 and the SH0ES collaboration measurements. After showing the H 0 evaluations made from different teams using different methods and geometric calibrations, we list a few interesting new physics models that could alleviate this tension and discuss how the next decade's experiments will be crucial. Moreover, we focus on the tension of the Planck CMB data with weak lensing measurements and redshift surveys, about the value of the matter energy density Ω m , and the amplitude or rate of the growth of structure ( σ 8 , f σ 8 ). We list a few interesting models proposed for alleviating this tension, and we discuss the importance of trying to fit a full array of data with a single model and not just one parameter at a time. Additionally, we present a wide range of other less discussed anomalies at a statistical significance level lower than the H 0 – S 8 tensions which may also constitute hints towards new physics, and we discuss possible generic theoretical approaches that can collectively explain the non-standard nature of these signals. Finally, we give an overview of upgraded experiments and next-generation space missions and facilities on Earth that will be of crucial importance to address all these open questions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe 4S] Fd activity

Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1 T11I ). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1 T11I . Electrochemical characterization revealed both Fer1 and Fer1 T11I have similar redox transitions (–480 mV and – 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron-sulfur (Fe—S) cluster of Fer1. Additionally, disruption of hydrogen bonding around an Fe—S cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1 T11I . Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1 T11I , which indicate changes to the high spin states and/or spin-spin coupling between the Fe—S clusters of Fer1. Finally, our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains: Implications for Actin Filament Nucleation

Actin filament nucleators initiate polymerization in cells in a regulated manner. A common architecture among these molecules consists of tandem WASP homology 2 domains (W domains) that recruit three to four actin subunits to form a polymerization nucleus. We describe a low-resolution crystal structure of an actin dimer assembled by tandem W domains, where the first W domain is cross-linked to Cys374 of the actin subunit bound to it, whereas the last W domain is followed by the C-terminal pointed end-capping helix of thymosin {beta}4. While the arrangement of actin subunits in the dimer resembles that of a long-pitch helix of the actin filament, important differences are observed. These differences result from steric hindrance of the W domain with intersubunit contacts in the actin filament. We also determined the structure of the first W domain of Vibrio parahaemolyticus VopL cross-linked to actin Cys374 and show it to be nearly identical with non-cross-linked W-Actin structures. This result validates the use of cross-linking as a tool for the study of actin nucleation complexes, whose natural tendency to polymerize interferes with most structural methods. Combined with a biochemical analysis of nucleation, the structures may explain why nucleators based on tandem W domains with short inter-W linkers have relatively weak activity, cannot stay bound to filaments after nucleation, and are unlikely to influence filament elongation. The findings may also explain why nucleation-promoting factors of the Arp2/3 complex, which are related to tandem-W-domain nucleators, are ejected from branch junctions after nucleation. We finally show that the simple addition of the C-terminal pointed end-capping helix of thymosin {beta}4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.

59 BASIC BIOLOGICAL SCIENCES↗

The Use of Positrons to Survey Alteration Layers on Synthetic Nuclear Waste Glasses

In order to safeguard society and the environment, understanding radioactive waste glass alteration mechanisms in interactions with solutions and near-field materials, such as Fe, is essential to nuclear waste repository performance assessments. Alteration products are formed at the surface of glasses after reaction with solution. In this study, glass altered in the presence of Fe0 in aqueous solution formed two alteration layers: one embedded with Fe closer to the surface and one without Fe found deeper in the sample. Both layers were found to be thinner than the alteration layer found in glass altered in aqueous solution only. For the first time, Doppler Broadening Positron Annihilation Spectroscopy (DB-PAS) is used to non-destructively characterize the pore structures of glass altered in the presence of Fe0. Advantages and disadvantages of DB-PAS compared to other techniques used to analyze pore structures for altered glass samples are discussed. Ultimately, DB-PAS has shown to be an excellent choice for pore structure characterization for glasses with multiple alteration layers. Monte Carlo modeling predicted positron trajectories through the layers, and helped explain DB-PAS data, which showed that the deeper alteration layer without Fe had a similar composition and pore structure to layers on glass altered in water only.

Doppler Broadening Positron Annihilation Spectrosc↗

Mechanisms of radiation-induced segregation around He bubbles in a Fe-Cr-Ni crystal

We report that Fe-15Cr-15Ni (wt.%) austenitic stainless steel was irradiated with 200 keV 4 He + ions to a fluence of 5 × 10 16 /cm 2 at 500 °C. Radiation-induced segregation (RIS) at He bubbles in the irradiated steel was measured using Energy Dispersive X-ray Spectroscopy (EDS) coupled with Scanning Transmission Electron Microscopy (STEM). The RIS measurements exhibited an enrichment of Ni and a depletion of Cr and Fe at the bubbles. To determine the underlying mechanisms of the RIS, the prediction of the Marwick model was compared with the RIS measurements. The model with parametric input in accordance with the Inverse Kirkendall effect (IKE), i.e. a preferential flux of elements associated with vacancy flux, was inadequate in explaining the observed amount of segregation of Fe, Cr and Ni. More specifically, a considerably lower ratio of the concentration gradient between Cr and Fe, $\left(\frac{∇Cr}{∇Fe}\right)$, of 0.53 was obtained from the RIS measurements versus the model-predicted value of 2.3, indicating an overestimation of Cr depletion at the bubbles by the Marwick model. To explain this difference between the model prediction and the RIS measurements, in addition to the Cr depletion at the bubbles by IKE due to the fastest diffusion via vacancy flux, a preferential interstitial flux of Cr from the matrix to the bubbles is discussed as a possible concurrently operating mechanism.

36 MATERIALS SCIENCE↗

Effect of friction stir welding and self-ion irradiation on dispersoid evolution in oxide dispersion strengthened steel MA956 up to 25 dpa

Here, the effect of ion irradiation on the microstructure of oxide dispersion strengthened (ODS) MA956 steel, before and after friction stir welding (FSW), was studied. Both the base material (BM) and welded stir zone (SZ) were irradiated with 5 MeV Fe ++ ions at 450 °C up to 25 displacements per atom (dpa). Characterization was performed using scanning transmission electron microscopy (STEM) and atom probe tomography (APT), with particular emphasis on the Y—Al—O dispersoid characteristics and dislocation microstructures. After irradiation, the dispersoids in the BM increased in diameter and decreased in number density, which was explained by an Ostwald ripening mechanism. FSW caused significant coarsening and agglomeration of the dispersoids. After irradiation, both the diameter and number density of the SZ dispersoids increased, which was explained by an irradiation-enhanced diffusion mechanism. Dislocation loop and network behavior was also characterized and large dislocation loops of ≈20 nm diameter formed by 1 dpa in both the BM and SZ samples, whereas the network density remained nearly constant with irradiation.

36 MATERIALS SCIENCE↗

Global and local texture development during initial plastic deformation of cold-pilgered Zircaloy-4 tubing

In this work we present a thorough characterization of the texture development during the initial step of a cold pilgering process of a Zircaloy-4 TREX tube, on which the axial cross section is reduced by 80% over a 40cm length with an overall Q-ratio of 2.34, followed by a recrystallization thermal treatment. Texture across a tapered specimen representing this working zone was characterized by neutron diffraction and high energy synchrotron x-ray diffraction at 28 positions (4 locations along its length and 7 locations across its thickness with 0.3 mm spatial resolution), and on the deformed end after the thermal treatment. Results show that the starting material (TREX tube) presents a texture gradient through its wall thickness, with the c poles aligned to the hoop direction at the outer surface (with radial and hoop Kearns factors: f R =0.36, f H = 0.50), and gradually rotating around the axial direction to become a quasi-radial orientation (~35 o out of the radial direction) at the inner surface ( f R =0.43, f H =0.35). The overall texture becomes more radial due to the cold pilgering, but the texture gradient remains during the whole deformation process, being always more radial at the inner surface, ( f R =0.53, f H =0.37 at 80%) than at the outer surface ( f R =0.41, f H =0.50at 80%). The most remarkable changes in texture produced by the rolling process is a 30 o rotation of the grains around their c-axis, producing a marked increase of the <11 2 ¯ 0> // axial fiber texture at expenses of the original <10 1 ¯ 0> // axial fiber texture observed in the TREX tube. The observed changes in texture during deformation were correctly explained by visco-plastic self-consistent (VPSC) modelling. This was achieved after the inclusion of the basal <a> slip system, which plays a central role to explain the 30 o rotation around the c-axis during deformation. The texture evolution was correctly described after the inclusion of a drag effect to grain rotation due to the interaction with neighbouring grains. The through thickness texture differences are greatly reduced by the recrystallization thermal treatment, with similar Kearns factors at the inner surface ( f R =0.50, f H =0.28) and the outer surface ( f R =0.48, f H =0.39). The predominance of the <10 1 ¯ 0> // axial fiber texture is recovered after recrystallization.

36 MATERIALS SCIENCE↗

Interpreting experimental measurements of helium bubbles using stochastic cluster dynamics models of heterogeneous nucleation and growth in irradiated ferritic alloys

Among a number of other advantageous features, ferritic/martensitic steels are being considered as fusion reactor structural materials due to their low intrinsic swelling under irradiation. However, under high-energy neutron irradiation, He produced through (n, α) reactions stabilizes vacancy clusters, which then act as seeds for bubble formation and growth, negating the intrinsic swelling resistance of these alloys. Standard models of irradiation damage accumulation and microstructural evolution consider homogeneous nucleation as the basis for bubble formation and growth. However, this generally does not explain the large bubble densities and sizes observed experimentally under a number of different conditions. Here, we propose a more realistic physical model of bubble nucleation, formation, and growth designed to capture recent experimental measurements of He-bubble formation and evolution during co-implantation of He and Fe ions in model ferritic alloys. We find that experimental results are explained only when the following three features are considered simultaneously: (i) heterogeneous nucleation of He-vacancy bubbles at defect sinks (e.g., dislocations, grain boundaries, and second-phase precipitates), (ii) nucleation and growth of bubbles via the ‘trap mutation’ mechanism (i.e., spontaneous production of Frenkel pairs due to absorption of He atoms), and (iii) transition from a growth-limited, He-stabilized bubble regime to a ‘runaway’ void-type growth scenario. The model is implemented into a stochastic cluster dynamics framework that takes advantage of cluster size grouping methods to accelerate the simulations, allowing us to reach 10 dpa of simulated irradiated dose, and to capture cluster sizes in excess of 20 nm. Further, a careful extrapolation exercise conducted assuming classical nucleation theory leads to excellent agreement with the experimental measurements at 50 dpa of irradiation.

36 MATERIALS SCIENCE↗

Electrochemical Reactions Under Reverse Bias Create Additional Mobile Ions That Enable Hole Tunneling in Metal Halide Perovskite Diodes

Gradual reverse-bias breakdown in metal-halide perovskite diodes and solar cells is thought to originate from hole tunneling through steep bands in an ionic depletion region near the electron-transport layer after positively charged iodine vacancies accumulate near the hole-transport layer (HTL). However, typical reported mobile-ion concentrations near 1 x 10^17 cm-3 are too small to quantitatively explain significant tunneling-current densities and (Zener) breakdown observed near -5 V. Here, we show that inferred mobile-ion concentrations increase by more than 100x, to over 1 x 10^18cm-3 , within just 3 min of reverse bias at -6.0 V in p-i-n perovskite diodes. We attribute this increase to iodide oxidation and coupled iodine vacancy creation that must be balanced by reduction reactions near the HTL. Sub-optimal HTL coverage leads to direct contact between the transparent conducting electrode and perovskite, facilitates reduction events, enables the creation of even larger inferred mobile-ion concentrations (~1 x 10^19cm-3 ), and leads to faster degradation under reverse bias. This explains previous work that showed increased breakdown voltages and improved reverse-bias stability by implementing thick, uniform HTLs.

14 SOLAR ENERGY↗

A combined theoretical-experimental study of interactions between vanadium ions and Nafion membrane in all-vanadium redox flow batteries

Vanadium redox flow batteries (VRFBs) are a promising solution for large-scale energy storage, but a number of problems still impede the deployment of long-lifetime VRFBs. One important aspect of efficient operation of VRFBs is understanding interactions between vanadium species and the membrane. Herein, we investigate the interactions between all four vanadium cations and Nafion membrane by a combination of infrared (IR) spectroscopy and density-functional-theory (DFT)-based static and molecular dynamics simulations. It is observed that vanadium species primarily lead to changes in the IR spectrum of Nafion in the SO 3 - spectral region which is attributed to the interaction between vanadium species and the SO 3 - exchange sites. DFT calculations of vanadium - Nafion complexes in the gas phase show that it is thermodynamically favorable for all vanadium cations to bind to SO 3 - via a contact pair mechanism. Car-Parrinello molecular dynamics-based metadynamics simulations of cation-Nafion systems in aqueous solution suggest that and species coordinate spontaneously to SO 3 - , which is not the case for VO 2+ and VO 2 + . The interaction behavior of the uncycled membrane determined in this study is used to explain the experimentally observed changes in the vibrational spectra, and is discussed in light of previous results on device-cycled membranes.

00-01↗