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Constrained optimization framework for interface-aware sub-scale dynamics models for voids closure in Lagrangian hydrodynamics
In hydrocodes, voids are used to represent vacuum and model free boundaries between vacuum and real materials. We give a systematic description of a new treatment of void closure in the framework of the multimaterial arbitrary Lagrangian–Eulerian (ALE) methods. This includes a new formulation of the interface-aware sub-scale-dynamics (IA-SSD) closure model for multimaterial cells with voids, which is used in the Lagrangian stage of our indirect ALE scheme. The results of the comprehensive testing of the new model are presented for one- and two-dimensional multimaterial calculations in the presence of voids. Finally, we also present a sneak peek of a realistic shaped charge calculation in the presence of voids and solids.
Self-irradiation and oxidation effects on americium sesquioxide and Raman spectroscopy studies of americium oxides
Americium oxides samples were characterized by X-ray diffraction (XRD) and Raman spectroscopy, with an emphasis on their structural behavior under oxidation and self-irradiation. Raman spectra of americium dioxide (AmO{sub 2}) and sesquioxide (Am{sub 2}O{sub 3}) were obtained for the first time. With the help of literature data on isostructural oxides, Raman signatures of Ia-3 C-type Am{sub 2}O{sub 3} and P-3m1 A-type Am{sub 2}O{sub 3} are identified. For AmO{sub 2,} a clear band is noted at 390 cm{sup −1}. Its nature is compared to that of the other actinide dioxides. Am{sub 2}O{sub 3} evolution under ambient conditions and against {sup 241}Am α self-irradiation was monitored by powder XRD. The sample, initially composed of A-type Am{sub 2}O{sub 3} as major phase as well as C2/m B-type and C-type structures as minor phases, progressively oxidizes to Fm-3m AmO{sub 2−δ} over a few months. On the basis of diffractogram refinements, evolutions of unit cell volumes caused by self-irradiation are also determined and discussed. - Graphical abstract: The evolution of americium oxide under ambient conditions was monitored using XRD (X-ray diffraction) and Raman spectroscopy. After a thermal treatment under reducing conditions, a polyphasic sample mainly composed of A- and C-type americium sesquioxides is evidenced by XRD and Raman spectroscopy. The sample then evolves through two processes: oxidation and self-irradiation. The first one provokes the progressive appearance of F-type americium dioxide while the initial phases disappear, whereas the main effect of the second is a structural swelling with time. - Highlights: • The first Raman spectroscopy measurements on americium oxides were performed. • Observed Am{sub 2}O{sub 3} Raman bands were identified thanks to data on analogue compounds. • AmO{sub 2} assumed T{sub 2g} band presents a shift compared to the actinide dioxide series. • Am{sub 2}O{sub 3} evolution under self-irradiation and oxidation was also monitored by XRD. • The three Am{sub 2}O{sub 3} phases observed have different behaviors under self-irradiation.
The solubility and site preference of Fe{sup 3+} in Li{sub 7−3x}Fe{sub x}La{sub 3}Zr{sub 2}O{sub 12} garnets
A series of Fe{sup 3+}-bearing Li{sub 7}La{sub 3}Zr{sub 2}O{sub 12} (LLZO) garnets was synthesized using solid-state synthesis methods. The synthetic products were characterized compositionally using electron microprobe analysis and inductively coupled plasma optical emission spectroscopy (ICP-OES) and structurally using X-ray powder diffraction and {sup 57}Fe Mössbauer spectroscopy. A maximum of about 0.25 Fe{sup 3+} pfu could be incorporated in Li{sub 7−3x}Fe{sub x}La{sub 3}Zr{sub 2}O{sub 12} garnet solid solutions. At Fe{sup 3+} concentrations lower than about 0.16 pfu, both tetragonal and cubic garnets were obtained in the synthesis experiments. X-ray powder diffraction analysis showed only a garnet phase for syntheses with starting materials having intended Fe{sup 3+} contents lower than 0.52 Fe{sup 3+} pfu. Back-scattered electron images made with an electron microprobe also showed no phase other than garnet for these compositions. The lattice parameter, a{sub 0}, for all solid-solution garnets is similar with a value of a{sub 0}≈12.98 Å regardless of the amount of Fe{sup 3+}. {sup 57}Fe Mössbauer spectroscopic measurements indicate the presence of poorly- or nano-crystalline FeLaO{sub 3} in syntheses with Fe{sup 3+} contents greater than 0.16 Fe{sup 3+} pfu. The composition of different phase pure Li{sub 7−3x}Fe{sub x}La{sub 3}Zr{sub 2}O{sub 12} garnets, as determined by electron microprobe (Fe, La, Zr) and ICP-OES (Li) measurements, give Li{sub 6.89}Fe{sub 0.03}La{sub 3.05}Zr{sub 2.01}O{sub 12}, Li{sub 6.66}Fe{sub 0.06}La{sub 3.06}Zr{sub 2.01}O{sub 12}, Li{sub 6.54}Fe{sub 0.12}La{sub 3.01}Zr{sub 1.98}O{sub 12}, and Li{sub 6.19}Fe{sub 0.19}La{sub 3.02}Zr{sub 2.04}O{sub 12}. The {sup 57}Fe Mössbauer spectrum of cubic Li{sub 6.54}Fe{sub 0.12}La{sub 3.01}Zr{sub 1.98}O{sub 12} garnet indicates that most Fe{sup 3+} occurs at the special crystallographic 24d position, which is the standard tetrahedrally coordinated site in garnet. Fe{sup 3+} in smaller amounts occurs at a general 96h site, which is only present for certain Li-oxide garnets, and in Li{sub 6.54}Fe{sub 0.12}La{sub 3.01}Zr{sub 1.98}O{sub 12} this Fe{sup 3+} has a distorted 4-fold coordination. - Graphical abstract: Cubic nominally Li{sub 7}La{sub 3}Zr{sub 2}O{sub 12} (LLZO) garnet is a promising candidate to be used as a solid electrolyte in Li-ion batteries. A series of Fe{sup 3+}-bearing LLZO garnets was synthesized and characterized compositionally and structurally. {sup 57}Mössbauer measurements were made to determine where Fe is incorporated in the crystal structure. X-ray diffraction, electron microprobe, ICP-OES and {sup 57}Mössbauer measurements are needed to obtain a full description of the synthetic products, some of which contain small amounts of nano- or poorly crystalline FeLaO{sub 3}. - Highlights: • A series of Fe{sup 3+}-bearing Li{sub 7}La{sub 3}Zr{sub 2}O{sub 12} (LLZO) garnets was synthesized and characterized compositionally and structurally. • {sup 57}Mössbauer measurements were made to determine where Fe is incorporated in the crystal structure. • Most Fe{sup 3+} substitutes for Li{sup +} in LLZO at the 24d and 96h sites in the cubic phase (Ia-3d). • No more than about 0.25 Fe{sup 3+} pfu can be incorporated into the LLZO garnet structure. • X-ray powder diffractions measurements indicate the presence of both cubic and tetragonal garnets phases in some syntheses. • The probable presence of small amounts of poorly or nano-crystalline FeLaO3 can only be identified by Mössbauer spectroscopy.
Syntheses, structure and magnetic properties of two vanadate garnets Ca{sub 5}M{sub 4}V{sub 6}O{sub 24} (M=Co, Ni)
Two vanadate compounds Ca{sub 5}M{sub 4}V{sub 6}O{sub 24} (M=Co, Ni) have been synthesized by a high-temperature solid-state reaction. The compounds are found to crystallize in the cubic system with a space group Ia-3d, which exhibit a typical garnet structural framework. Magnetic measurements show that Ca{sub 5}M{sub 4}V{sub 6}O{sub 24} (M=Co, Ni) exhibit similar magnetic behaviors, in which Ca{sub 5}Co{sub 4}V{sub 6}O{sub 24} possesses an antiferromagnetic ordering at T{sub N}=~6 K while Ca{sub 5}Ni{sub 4}V{sub 6}O{sub 24} shows an antiferromagnetic ordering at T{sub N}=~7 K. - Graphical abstract: Garnet vanadate compounds Ca{sub 5}M{sub 4}V{sub 6}O{sub 24} (M=Co, Ni) have been synthesized by a high-temperature solid-state reaction. Structural features and magnetic behaviors are also investigated. - Highlights: • New type of garnet vanadates Ca{sub 5}M{sub 4}V{sub 6}O{sub 24} (M=Co, Ni) are synthesized by a high-temperature solid-state reaction. • Structural features are confirmed by single crystal samples. • Magnetic behaviors are firstly investigated in the systems.
Nuclear Data Sheets for A = 43
The experimental data are evaluated for known nuclides of mass number A = 43 (Al,Si,P,S,Cl,Ar,K,Ca,Sc,Ti,V,Cr). Detailed evaluated level properties and related information are presented, including adopted values of level and γ–ray energies, decay data (energies, intensities and placement of radiations), and other spectroscopic data. Here, this work supersedes earlier full evaluations of A = 43 published by 2001Ca24 and 1990En08 (also 1978En04, and 1998En04 update).
SNAD transient miner: Finding missed transient events in ZTF DR4 using k-D trees
Here we report the automatic detection of 11 transients (7 possible supernovae and 4 active galactic nuclei candidates) within the Zwicky Transient Facility fourth data release (ZTF DR4), all of them observed in 2018 and absent from public catalogs. Among these, three were not part of the ZTF alert stream. Our transient mining strategy employs 41 physically motivated features extracted from both real light curves and four simulated light curve models (SN Ia, SN II, TDE, SLSN-I). These features are input to a k-D tree algorithm, from which we calculate the 15 nearest neighbors. After pre-processing and selection cuts, our dataset contained approximately a million objects among which we visually inspected the 105 closest neighbors from seven of our brightest, most well-sampled simulations, comprising 89 unique ZTF DR4 sources. Our result illustrates the potential of coherently incorporating domain knowledge and automatic learning algorithms, which is one of the guiding principles directing the SNAD team. It also demonstrates that the ZTF DR is a suitable testing ground for data mining algorithms aiming to prepare for the next generation of astronomical data.
Duality between ( 2 + 1 ) d quantum critical points
We describe the simulated data sample for the “Photometric LSST Astronomical Time Series Classi-fication Challenge” (PLAsTiCC), a publicly available challenge to classify transient and variable eventsthat will be observed by the Large Synoptic Survey Telescope (LSST), a new facility expected tostart in the early 2020s. The challenge was hosted by Kaggle, ran from 2018 September 28 to 2018December 17, and included 1,094 teams competing for prizes. Here we provide details of the 18 tran-sient and variable source models, which were not revealed until after the challenge, and release themodel libraries athttps://doi.org/10.5281/zenodo.2612896. We describe the LSST OperationsSimulator used to predict realistic observing conditions, and we describe the publicly availableSNANAsimulation code used to transform the models into observed fluxes and uncertainties in the LSSTpassbands (ugrizy). AlthoughPLAsTiCChas finished, the publicly available models and simulationtools are being used within the astronomy community to further improve classification, and to studycontamination in photometrically identified samples of type Ia supernova used to measure propertiesof dark energy. Our simulation framework will continue serving as a platform to improve thePLAsTiCCmodels, and to develop new models.
Oxidative DNA damage and repair in children exposed to low levels of arsenic in utero and during early childhood: Application of salivary and urinary biomarkers
The present study aimed to assess arsenic exposure and its effect on oxidative DNA damage and repair in young children exposed in utero and continued to live in arsenic-contaminated areas. To address the need for biological specimens that can be acquired with minimal discomfort to children, we used non-invasive urinary and salivary-based assays for assessing arsenic exposure and early biological effects that have potentially serious health implications. Levels of arsenic in nails showed the greatest magnitude of difference between exposed and control groups, followed by arsenic concentrations in saliva and urine. Arsenic levels in saliva showed significant positive correlations with other biomarkers of arsenic exposure, including arsenic accumulation in nails (r = 0.56, P < 0.001) and arsenic concentration in urine (r = 0.50, P < 0.05). Exposed children had a significant reduction in arsenic methylation capacity indicated by decreased primary methylation index and secondary methylation index in both urine and saliva samples. Levels of salivary 8-OHdG in exposed children were significantly higher (∼ 4-fold, P < 0.01), whereas levels of urinary 8-OHdG excretion and salivary hOGG1 expression were significantly lower in exposed children (∼ 3-fold, P < 0.05), suggesting a defect in hOGG1 that resulted in ineffective cleavage of 8-OHdG. Multiple regression analysis results showed that levels of inorganic arsenic (iAs) in saliva and urine had a significant positive association with salivary 8-OHdG and a significant negative association with salivary hOGG1 expression. - Highlights: • The effects of arsenic exposure in utero and through early childhood were studied. • Arsenic-exposed children had a reduction in arsenic methylation capacity. • Exposed children had more DNA damage, observed as elevated salivary 8-OHdG. • Lower salivary hOGG1 in exposed children indicated impairment of 8-OHdG repair. • Salivary and urinary 8-OHdG levels were discordant.
Transient and permanent changes in DNA methylation patterns in inorganic arsenic-mediated epithelial-to-mesenchymal transition
Chronic low dose inorganic arsenic exposure causes cells to take on an epithelial-to-mesenchymal phenotype, which is a crucial process in carcinogenesis. Inorganic arsenic is not a mutagen and thus epigenetic alterations have been implicated in this process. Indeed, during the epithelial-to-mesenchymal transition, morphologic changes to cells correlate with changes in chromatin structure and gene expression, ultimately driving this process. However, studies on the effects of inorganic arsenic exposure/withdrawal on the epithelial-to-mesenchymal transition and the impact of epigenetic alterations in this process are limited. In this study we used high-resolution microarray analysis to measure the changes in DNA methylation in cells undergoing inorganic arsenic-induced epithelial-to-mesenchymal transition, and on the reversal of this process, after removal of the inorganic arsenic exposure. We found that cells exposed to chronic, low-dose inorganic arsenic exposure showed 30,530 sites were differentially methylated, and with inorganic arsenic withdrawal several differential methylated sites were reversed, albeit not completely. Furthermore, these changes in DNA methylation mainly correlated with changes in gene expression at most sites tested but not at all. This study suggests that DNA methylation changes on gene expression are not clear-cut and provide a platform to begin to uncover the relationship between DNA methylation and gene expression, specifically within the context of inorganic arsenic treatment. - Highlights: • Transient and permanent methylation patterns are modulated by iAs exposure. • Arsenite contributes to the epithelial-to-mesenchymal transition. • Arsenite mediated epigenetic changes play a role in EMT.
Order/Disorder and in Situ Oxide Defect Control in the Bixbyite Phase YPrO 3+δ (0 ≤ δ < 0.5)
The YPrO 3+δ system is a nearly ideal model system for the investigation of oxide defect creation and annihilation in oxide ion conductor related phases with potential applications as solid state electrolytes in solid oxide fuel cells. The formation, structure, high temperature reactivity, and magnetic susceptibility of phase pure YPrO 3+δ (0 ≤ δ ≤ 0.46) are reported. The topotactic reduction and oxidation of the YPrO 3+δ system was investigated by powder X-ray in situ diffraction experiments and revealed bixbyite structures (space group: $Ia\bar{3}$) throughout the series. Combined neutron and X-ray data clearly show oxygen uptake and removal. The research provides a detailed picture of the Y 3+ /Pr 3+ /Pr 4+ sublattice evolution in response to the redox chemistry. Upon oxidation, cation site splitting is observed where the cation in the (1/4, 1/4, 1/4) position migrates along the body diagonal to the (x, x, x) position. Any oxygen in excess of YPrO 3.0 is located in the additional 16c site without depopulating the original 48e site. The in situ X-ray diffraction data and thermal gravimetric analysis have revealed the reversible topotactic redox reactivity at low temperatures (below 425 °C) for all compositions from YPrO 3 to YPrO 3.46 . Magnetic susceptibility studies were utilized in order to further confirm praseodymium oxidation states. The linear relation between the cubic unit cell parameter and oxygen content allows for the straightforward determination of oxygen stoichiometry from X-ray diffraction data. Here, the different synthesis strategies reported here are rationalized with the structural details and the reactivity of YPrO 3+δ phases and provide guidelines for the targeted synthesis of these functional materials.
Mössbauer Spectral Properties of Yttrium Iron Garnet, Y3Fe5O12, and its Isovalent and Nonisovalent Yttrium-Substituted Solid Solutions
Several high-resolution Mössbauer spectra of yttrium iron garnet, Y3Fe5O12, have been fit as a function of temperature with a new model based on a detailed analysis of the spectral changes that result from a reduction from the cubic Ia–3d space group to the trigonal R–3 space group. These spectral fits, which are all statistically identical, indicate that the magnetic sextet arising from the 16a site in cubic symmetry is subdivided into three sextets arising from the 6f, and the 3d, 3d, and the 1a, 1b, and 2c sites in rhombohedral-axis trigonal symmetry. The 24d site in cubic symmetry is subdivided into four sextets arising from four different 6f sites in R–3 rhombohedral-axis trigonal symmetry, sites that differ only by the angles between the principal axis of the electric field gradient tensor and the magnetic hyperfine field assumed to be parallel with the magnetic easy axis. This analysis, when applied to the potential nuclear waste storage compounds, Y3-xCa0.5xTh0.5xFe5O12 and Y3- xCa0.5xCe0.5xFe5O12, indicates virtually no perturbation of the structural, electronic, and magnetic properties upon substitution of small amounts of calcium(II) and thorium(IV) or cerium(IV) onto the yttrium(III) 24c site as compared with Y3Fe5O12. The observed broadening of the four different 6f sites derived from the 24d site results from the substitution of yttrium(III) by calcium(II) and thorium(IV) or cerium(IV) cations on the next-nearest neighbor 24c site. In contrast, the same analysis, when applied to Y2.8Ce0.2Fe5O12, indicates a local perturbation of the magnetic exchange pathways as a result of the presence of cerium(IV) in the 24c next-nearest neighbor site of the iron(III) 24d site.
Nonadiabatic Dynamics in a Continuous Circularly Polarized Laser Field with Floquet Phase-Space Surface Hopping
Non-adiabatic chemical reactions involving continuous circularly polarized light (cw CPL) have not attracted as much attention as dynamics in unpolarized/linearly polarized light. However, including circularly (in contrast to linearly) polarized light allows one to effectively introduce a complex-valued time-dependent Hamiltonian, which offers a new path for control or exploration through the introduction of Berry forces. Here, we investigate several inexpensive semiclassical approaches for modeling such nonadiabatic dynamics in the presence of a time-dependent complex-valued Hamiltonian, beginning with a straightforward instantaneous adiabatic fewest-switches surface hopping (IA-FSSH) approach (where the electronic states depend on position and time), continuing to a standard Floquet fewest switches surface hopping (F-FSSH) approach (where the electronic states depend on position and frequency), and ending with an exotic Floquet phase-space surface hopping (F-PSSH) approach (wherethe electronic states depend on position, frequency, and momentum). Using a set of model systems with time-dependent complex-valued Hamiltonians, we show that the Floquet phase- space adiabats are the optimal choice of basis as far as accounting for Berry phase effects and delivering accuracy. Furthermore, the F-PSSH algorithm sets the stage for modeling nonadiabatic dynamics under strong externally pumped circular polarization in the future.
Generating Bright Emissive States by Modulating the Bandgap of Monolayer Tungsten Diselenide
Transition metal dichalcogenides (TMDs) are essential due to their fascinating electronic and optical properties, strong exciton binding energy, and layer-dependent bandgap. They can be tuned to function as a single-photon emitter, but the quantum yield of photoluminescence of single-layer WSe 2 is low. There is some evidence that a bright emissive state can be produced by introducing local defects through functionalization. In this paper we use spin-polarized periodic density functional theory (DFT) to study the effect of functionalization for the specific case of cyclic carbenes. We find that the simplest of these molecules, cyclopentadiene carbene (Cyc), binds to the surface by a covalent bond leading to a substantial change in the bandgap (1.24 eV compared to 1.64 eV for the pristine surface). Moreover, there are semiflat bands below the Fermi level that originate from σ bonding and the interaction between the lone-pair p orbitals on the carbon of Cyc that bonds with Se on the TMD. Cyc is found to form a Type IIa heterojunction before and after contact with the surface, where the “a” refers to ordering of the energy levels where the TMD levels have the larger splitting and “b” to the reverse. The effect of various electron-withdrawing and electron-donating groups on Cyc is investigated, and it is found that the direct bandgap and heterointerfaces can be chemically tuned with covalently bound functional groups. With an electron-withdrawing group (EWG) such as –CHO, –COCl, and –CN attached to Cyc, a Type III//Type IIa interface is formed, whereas all other EWGs used in this study form a Type IIa junction, before and after contact to the surface. The electron-donating groups (EDG) form Type Ib//Type Ia junctions, and in particular, we find that the system WSe 2 + Cyc-Me band structure consists of semiflat bands at valence band maxima localized on Cyc-Me and the conduction band minimum is coupled between the surface and functional group with a direct bandgap of 0.88 eV. Hence, we predict that the Cyc-Me-functionalized monolayer WSe 2 will produce a red-shifted bright emissive state. Furthermore, we also find that carbenes with the Cyc all-carbon ring have (1) a triplet ground state and (2) form covalent bonds to WSe 2 , while heterocyclic carbenes (1) have a singlet ground state and (2) do not form covalent bonds to WSe 2 .
In Situ Electron Microscopy Investigation of Sodiation of Titanium Disulfide Nanoflakes
Two-dimensional (2D) metal sulfides show great promises for their potential applications as electrode materials of sodium ion batteries because of the weak interlayer van der Waals interactions which allow the reversible accommodation and extraction of sodium ions. The sodiation of metal sulfides can undergo a distinct process compared to that of lithiation, which is determined by their metal and structural types. Yet, the structural and morphological evolution during its electrochemical sodiation is still unclear. In this report, we studied the sodiation reaction dynamics of TiS 2 by employing in situ transmission electron microscopy and first-principles calculations. During the sodium ion intercalation process, we observed multiple intermediate phases (phase II, phase Ib, and phase Ia), different from its lithiation counterpart, with varied sodium occupation sites and interlayer stacking sequences. Further insertion of Na ions prompted a multi-step extrusion reaction which led to the phase separation of Ti metal from the Na 2 S matrix, with its 2D morphology expanded to a 3D morphology. In contrast to regular conversion electrodes, TiS 2 still maintained a compacted structure after a full sodiation. Frist-principles calculations reveal that the as-identified phases are thermodynamically preferred at corresponding intercalation/extrusion stages compared to other possible phases. The current work provides the fundamental mechanistic understanding of the sodiation process of 2D transition metal sulfides.
Toward Practical Carrier Multiplication: Donor/Acceptor Codoped Si Nanocrystals in SiO 2
Carrier multiplication (CM) is an interesting fundamental phenomenon with application potential in optoelectronics and photovoltaics, and it has been shown to be promoted by quantum confinement effects in nanostructures. However, mostly due to the short lifetimes of additional electron-hole (e-h) pairs generated by CM, major improvements of quantum dot devices that exploit CM are limited. Here we investigate CM in SiO2 solid state dispersions of phosphorus and boron codoped Si nanocrystals (NCs): an exotic variant of Si NCs whose photoluminescence (PL) emission energy, the optical bandgap, is significantly red-shifted in comparison to undoped Si NCs. By combining the results obtained by ultrafast induced absorption (IA) with PL quantum yield (PL QY) measurements, we demonstrate CM with a long (around 100 us) lifetime of the additional e-h pairs created by the process, similar as previously reported for undoped Si NCs, but with a significantly lower CM threshold energy. This constitutes a significant step toward the practical implementation of Si-based NCs in optoelectronic devices: we demonstrate efficient CM at the energy bandgap optimal for photovoltaic conversion.
Evidence That the [beta] Subunit of Chlamydia trachomatis Ribonucleotide Reductase Is Active with the Manganese Ion of Its Manganese(IV)/Iron(III) Cofactor in Site 1
The reaction of a class I ribonucleotide reductase (RNR) begins when a cofactor in the {beta} subunit oxidizes a cysteine residue {approx}35 {angstrom} away in the {alpha} subunit, generating a thiyl radical. In the class Ic enzyme from Chlamydia trachomatis (Ct), the cysteine oxidant is the Mn{sup IV} ion of a Mn{sup IV}/Fe{sup III} cluster, which assembles in a reaction between O{sub 2} and the Mn{sup II}/Fe{sup II} complex of {beta}. The heterodinuclear nature of the cofactor raises the question of which site, 1 or 2, contains the Mn{sup IV} ion. Because site 1 is closer to the conserved location of the cysteine-oxidizing tyrosyl radical of class Ia and Ib RNRs, we suggested that the Mn{sup IV} ion most likely resides in this site (i.e., {sup 1}Mn{sup IV}/{sup 2}Fe{sup III}), but a subsequent computational study favored its occupation of site 2 ({sup 1}Fe{sup III}/{sup 2}Mn{sup IV}). In this work, we have sought to resolve the location of the Mn{sup IV} ion in Ct RNR-{beta} by correlating X-ray crystallographic anomalous scattering intensities with catalytic activity for samples of the protein reconstituted in vitro by two different procedures. In samples containing primarily Mn{sup IV}/Fe{sup III} clusters, Mn preferentially occupies site 1, but some anomalous scattering from site 2 is observed, implying that both {sup 1}Mn{sup II}/{sup 2}Fe{sup II} and {sup 1}Fe{sup II}/{sup 2}Mn{sup II} complexes are competent to react with O{sub 2} to produce the corresponding oxidized states. However, with diminished Mn{sup II} loading in the reconstitution, there is no evidence for Mn occupancy of site 2, and the greater activity of these 'low-Mn' samples on a per-Mn basis implies that the {sup 1}Mn{sup IV}/{sup 2}Fe{sup III}-{beta} is at least the more active of the two oxidized forms and may be the only active form.
Author Correction: Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota
Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-024-53784-3, published online 4 November 2024 In the version of this article initially published, Table 1 did not include the properties of the taxa being proposed or refer directly to another location in the main manuscript describing the properties. As such, the original manuscript did not comply with Rule 27 (2)(c) of the ICNP. Also, Table 1 listed the order Fervidibacterales as the nomenclatural type for the class Fervidibacteria, which violates latest emended version of Rule 15 stating that the nomenclatural type for a class must be a genus. Below we provide a modification of Table 1 containing protologues with these errors corrected. We have also changed the order of the taxa in the table to meet the most common ordering. (Table presented.) Taxon names proposed under the ICNP Proposed taxon Etymology Description Genus Fervidibacter Fer.vi.di.bac’ter. L. masc. adj. fervidus, hot, steaming; N.L. masc. n. bacter, a rod; N.L. masc. n. Fervidibacter, a hot rod Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the genus. Gram-stain-negative and diderm cell envelope structure. Ovoid- to rod-shaped morphology. Spores are not formed. The genus is a distinct phylogenetic lineage in the family Fervidibacteraceae, the order Fervidibacterales, and the class Fervidibacteria in the phylum Armatimonadota. The type species is Fervidibacter sacchariT. Species Fervidibacter sacchari sac’cha.ri. N.L. gen. n. sacchari, of sugar Hyperthermophilic, microaerophilic, facultatively anaerobic, and grows chemoheterotrophically on monosaccharides and polysaccharides. Cells are ovoid- to rod-shaped, Gram-stain negative, and are 0.9–1.3 µm in width and 1.6–3.6 µm in length. Grows between 65 and 87.5 °C and an optimum temperature of 80 °C, and a pH range of 6.5–8.6 with an optimum pH of 7.5. Grows at an optimum O2 concentration of 5–10%. Grows on D-arabinose, D-galactose, D-glucose, D-rhamnose, D-ribose, D-xylose, chondroitin sulfate, colloidal chitin, galactan, gellan gum, guar gum, karaya gum, locust bean gum, xantham gum, xyloglucan, β-glucan, glycogen, starch, AFEX-pretreated corn stover, miscanthus, sugarcane bagasse, acetate and casamino acids. Grows weakly on xyloglucan under fermentation conditions. The major fatty acids (>10%) are C16:0, C18:0 and/or cyclo-C17:0, and iso-C16:0. The major respiratory quinones (>10%) are MK-8 and MK-9. The isolate and genomes of the species have been recovered from geothermal springs in the Great Basin, Nevada, USA. GC content of genomes range between 51–52%. Subunits for both the high-affinity and low-affinity terminal oxidases are encoded in the genomes. Genomes also encode a Group 3d [NiFe] hydrogenase, which produces hydrogen as an electron sink for NAD+ regeneration. The type strain PD1T (= JCM 39283T = DSM 113467T) was isolated from Great Boiling Spring in Nevada, USA. Family Fervidibacteraceae Fer.vi.di.bac.te.ra’ce.ae. N.L. masc. n. Fervidibacter type genus of the family; L. suff. -aceae ending to denote a family; N.L. fem. pl. n. Fervidibacteraceae the family of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the family. The family is a distinct phylogenetic lineage in the order Fervidibacterales and the class Fervidibacteria in the phylum Armatimonadota. The type genus is Fervidibacter. Order Fervidibacterales Fer.vi.di.bac.te.ra’les. N.L. masc. n. Fervidibacter type genus of the order; L. suff. -ales ending to denote an order; N.L. fem. pl. n. Fervidibacterales the order of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Fervidibacteria and relative evolutionary divergence supports delineation of this lineage as an order within the class Fervidibacteria and phylum Armatimonadota. The type genus is Fervidibacter. Class Fervidibacteria Fer.vi.di.bac.te’ri.a. N.L. masc. n. Fervidibacter type genus of the type order of the class; L. suff. -ia ending to denote a class; N.L. neut. pl. n. Fervidibacteria the class of the order Fervidibacterales Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Armatimonadota and relative evolutionary divergence supports delineation of this lineage as a class within the Armatimonadota. The type genus is Fervidibacter. 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