Oxide-ion diffusion in brownmillerite-type Ca2AlMnO5+δ from first-principles calculations.

Oxide-ion diffusion pathways in brownmillerite oxides Ca2AlMnO5 and Ca2AlMnO5.5 are systematically investigated using first-principles calculations. These structures reversibly transform into each other by oxidation and reduction. We examine oxide-ion migration in Ca2AlMnO5 and Ca2AlMnO5.5 using the nudged elastic band method. In the reduced structure (Ca2AlMnO5), oxide-ion migration through a vacancy channel is found to have the lowest migration energy barrier, at 0.58 eV. The migration energy barrier of the second-lowest energy path, perpendicular to the vacancy channel, is found to be 0.98 eV. In the oxidized structure (Ca2AlMnO5.5), oxide-ion migration within AlO6 layers has migration energy barriers of 0.55 eV and 0.56 eV in the [100] and [001] directions, respectively. Oxide-ion migration perpendicular to the AlO6 layer has a migration energy barrier of 1.33 eV, suggesting that oxide-ion diffusion in the [010] direction is difficult even at elevated temperature. These results indicate that diffusion in the reduced phase is predominantly one-dimensional whereas it is two-dimensional in the oxidized phase.

Combination of recommender system and single-particle diagnosis for accelerated discovery of novel nitrides.

Discovery of new compounds from wide chemical space is attractive for materials researchers. However, theoretical prediction and validation experiments have not been systematically integrated. Here, we demonstrate that a new combined approach is powerful in significantly accelerating the discovery rate of new compounds, which should be useful for exploration of a wide chemical space in general. A recommender system for chemically relevant composition is constructed by machine learning of Inorganic Crystal Structure Database using chemical compositional descriptors. Synthesis and identification experiments are made at the chemical compositions with high recommendation scores by the single-particle diagnosis method. Two new compounds, La4Si3AlN9 and La26Si41N80O, and two new variants (isomorphic substitutions) of known compounds, La7Si6N15 and La4Si5N10O, are successfully discovered. Finally, density functional theory calculations are conducted for La4Si3AlN9 to confirm the energetic and dynamical stability and to reveal its atomic arrangement.

Radiation dose for 320-row dose-modulated dynamic coronary CT angiography.

OBJECTIVES: The area detector 320-row CT scanner, which can cover the whole heart in one rotation, can aid in reducing radiation exposure during electrocardiography (ECG)-gated coronary CT angiography (CCTA). Recently, researchers have proposed dose-modulated dynamic CCTA with a 320-row scanner for the detection of functional myocardial ischemia. In the present study, we compared and validated the radiation dose of this method with that of the standard CCTA method and the latest diagnostic reference levels (DRLs). MATERIALS AND METHODS: The study included a total of 164 consecutive patients with suspected or known coronary artery disease (CAD) who underwent CCTA with a 320-row scanner. The patients were randomly divided into dynamic and standard CCTA groups, and the CT dose index (CTDIvol) and dose length product (DLP) calculated by the CT system were compared between the two protocols and with the latest DRL. RESULTS: Standard and dynamic CCTA scans were performed in 77 and 87 patients, respectively. CTDIvol was significantly higher for standard CCTA than for dynamic CCTA (41 ± 35 mGy vs. 22 ± 7 mGy, p = 0.0014). DLP was also significantly higher for standard CCTA than for dynamic CCTA (864 ± 702 mGy × cm vs. 434 ± 106 mGy × cm, p < .0001). For standard scans, CTDIvol and DLP exceeded the 2020 DRL in Japan in 16% (12/77) and 17% (13/77) of cases, respectively. In contrast, rates for the dynamic scan were only 1% (1/87) for CTDIvol and 0% (0/87) for DLP. CONCLUSION: The dose of radiation exposure during dynamic CCTA with a 320-row scanner does not exceed that of standard CCTA and is sufficient to meet the latest DRL. Thus, our results suggest that the method is safe from the perspective of radiation exposure.

Enumeration of nonequivalent substitutional structures using advanced data structure of binary decision diagram.

A derivative structure is a nonequivalent substitutional atomic configuration derived from a given primitive cell. The enumeration of derivative structures plays an essential role in searching for the ground states in multicomponent systems. However, it is computationally difficult to enumerate derivative structures if the number of derivative structures of a target system becomes huge. In this study, we introduce a novel compact data structure of the zero-suppressed binary decision diagram (ZDD) for enumerating derivative structures much more efficiently. We show its simple applications to the enumeration of structures derived from the face-centered cubic and hexagonal close-packed lattices in binary, ternary, and quaternary systems. The present ZDD-based procedure should contribute to computational approaches based on derivative structures in physics and materials science.

The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion.

Archaea and eukaryotes have ribosomal P stalks composed of anchor protein P0 and aP1 homodimers (archaea) or P1•P2 heterodimers (eukaryotes). These P stalks recruit translational GTPases to the GTPase-associated center in ribosomes to provide energy during translation. The C-terminus of the P stalk is known to selectively recognize GTPases. Here we investigated the interaction between the P stalk and elongation factor 2 by determining the structures of Pyrococcus horikoshii EF-2 (PhoEF-2) in the Apo-form, GDP-form, GMPPCP-form (GTP-form), and GMPPCP-form bound with 11 C-terminal residues of P1 (P1C11). Helical structured P1C11 binds to a hydrophobic groove between domain G and subdomain G' of PhoEF-2, where is completely different from that of aEF-1α in terms of both position and sequence, implying that such interaction characteristic may be requested by how GTPases perform their functions on the ribosome. Combining PhoEF-2 P1-binding assays with a structural comparison of current PhoEF-2 structures and molecular dynamics model of a P1C11-bound GDP form, the conformational changes of the P1C11-binding groove in each form suggest that in response to the translation process, the groove has three states: closed, open, and release for recruiting and releasing GTPases.

Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.

Tomato spotted wilt virus (TSWV), belonging to the genus Tospovirus of the family Bunyaviridae, causes significant economic damage to several vegetables and ornamental plants worldwide. Similar to those of all other negative-strand RNA viruses, the nucleocapsid (N) protein plays very important roles in its viral life cycle. N proteins protect genomic RNAs by encapsidation and form a viral ribonucleoprotein complex (vRNP) with some RNA-dependent RNA polymerases. Here we show the crystal structure of the N protein from TSWV. Protomers of TSWV N proteins consist of three parts: the N arm, C arm, and core domain. Unlike N proteins of other negative-strand RNA viruses, the TSWV N protein forms an asymmetric trimeric ring. To form the trimeric ring, the N and C arms of the N protein interact with the core domains of two adjacent N proteins. By solving the crystal structures of the TSWV N protein with nucleic acids, we showed that an inner cleft of the asymmetric trimeric ring is an RNA-binding site. These characteristics are similar to those of N proteins of other viruses of the family Bunyaviridae Based on these observations, we discuss possibilities of a TSWV encapsidation model.IMPORTANCE Tospoviruses cause significant crop losses throughout the world. Particularly, TSWV has an extremely wide host range (>1,000 plant species, including dicots and monocots), and worldwide losses are estimated to be in excess of $1 billion annually. Despite such importance, no proteins of tospoviruses have been elucidated so far. Among TSWV-encoded proteins, the N protein is required for assembling the viral genomic RNA into the viral ribonucleoprotein (vRNP), which is involved in various steps of the life cycle of these viruses, such as RNA replication, virus particle formation, and cell-to-cell movement. This study revealed the structure of the N protein, with or without nucleic acids, of TSWV as the first virus of the genus Tospovirus, so it completed our view of the N proteins of the family Bunyaviridae.

Crystal Structure and Superconductivity of Tetragonal and Monoclinic Ce1- xPr xOBiS2.

Ce1- xPr xOBiS2 powders and Ce0.5Pr0.5OBiS2 single crystals were synthesized and their structure and superconductive properties were examined by X-ray diffraction, X-ray absorption, electronic resistivity, and magnetization. While PrOBiS2 was found to be in a monoclinic phase with one-dimensional Bi-S zigzag chains showing no superconductive transition above 0.1 K, CeOBiS2 was in a tetragonal phase with two-dimensional Bi-S planes showing zero resistivity below 1.3 K. In the range x = 0.3-0.9 in Ce1- xPr xOBiS2, both monoclinic and tetragonal phases were formed together with zero resistivity up to a maximum temperature of 2.2 K. A Ce0.5Pr0.5OBiS2 single crystal, which showed both zero resistivity and a decrease in magnetization at ∼2.4 K, presented a tetragonal structure. Short Bi-S bonding in flat two-dimensional Bi-S planes and mixed Ce3+/Ce4+ were characteristic features of the Ce0.5Pr0.5OBiS2 single crystal, which presumably triggered its superconductivity.

Linearized machine-learning interatomic potentials for non-magnetic elemental metals: Limitation of pairwise descriptors and trend of predictive power.

Machine-learning interatomic potential (MLIP) has been of growing interest as a useful method to describe the energetics of systems of interest. In the present study, we examine the accuracy of linearized pairwise MLIPs and angular-dependent MLIPs for 31 elemental metals. Using all of the optimal MLIPs for 31 elemental metals, we show the robustness of the linearized frameworks, the general trend of the predictive power of MLIPs, and the limitation of pairwise MLIPs. As a result, we obtain accurate MLIPs for all 31 elements using the same linearized framework. This indicates that the use of numerous descriptors is the most important practical feature for constructing MLIPs with high accuracy. An accurate MLIP can be constructed using only pairwise descriptors for most non-transition metals, whereas it is very important to consider angular-dependent descriptors when expressing interatomic interactions of transition metals.

Compositional descriptor-based recommender system for the materials discovery.

Structures and properties of many inorganic compounds have been collected historically. However, it only covers a very small portion of possible inorganic crystals, which implies the presence of numerous currently unknown compounds. A powerful machine-learning strategy is mandatory to discover new inorganic compounds from all chemical combinations. Herein we propose a descriptor-based recommender-system approach to estimate the relevance of chemical compositions where crystals can be formed [i.e., chemically relevant compositions (CRCs)]. In addition to data-driven compositional similarity used in the literature, the use of compositional descriptors as a prior knowledge is helpful for the discovery of new compounds. We validate our recommender systems in two ways. First, one database is used to construct a model, while another is used for the validation. Second, we estimate the phase stability for compounds at expected CRCs using density functional theory calculations.

Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis.

Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNA(Asn), and instead synthesize asparagine from tRNA(Asn)-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNA(Asn), and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNA(Asn) to form Asn-tRNA(Asn) for use in protein synthesis. ND-AspRS, GatCAB, and tRNA(Asn) may assemble in an ∼400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNA(Asn). We report the 3.7-Šresolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNA(Asn) molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNA(Asn) formation evolutionarily preceded the direct attachment of Asn to tRNA(Asn), our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.

Impact of Chemical Fluctuations on Stacking Fault Energies of CrCoNi and CrMnFeCoNi High Entropy Alloys from First Principles.

Medium and high entropy alloys (MEAs and HEAs) based on 3d transition metals, such as face-centered cubic (fcc) CrCoNi and CrMnFeCoNi alloys, reveal remarkable mechanical properties. The stacking fault energy (SFE) is one of the key ingredients that controls the underlying deformation mechanism and hence the mechanical performance of materials. Previous experiments and simulations have therefore been devoted to determining the SFEs of various MEAs and HEAs. The impact of local chemical environment in the vicinity of the stacking faults is, however, still not fully understood. In this work, we investigate the impact of the compositional fluctuations in the vicinity of stacking faults for two prototype fcc MEAs and HEAs, namely CrCoNi and CrMnFeCoNi by employing first-principles calculations. Depending on the chemical composition close to the stacking fault, the intrinsic SFEs vary in the range of more than 150 mJ/m 2 for both the alloys, which indicates the presence of a strong driving force to promote particular types of chemical segregations towards the intrinsic stacking faults in MEAs and HEAs. Furthermore, the dependence of the intrinsic SFEs on local chemical fluctuations reveals a highly non-linear behavior, resulting in a non-trivial interplay of local chemical fluctuations and SFEs. This sheds new light on the importance of controlling chemical fluctuations via tuning, e.g., the annealing condition to obtain the desired mechanical properties for MEAs and HEAs.

Unconventional Superconductivity in the BiS_{2}-Based Layered Superconductor NdO_{0.71}F_{0.29}BiS_{2}.

We investigate the superconducting-gap anisotropy in one of the recently discovered BiS_{2}-based superconductors, NdO_{0.71}F_{0.29}BiS_{2} (T_{c}∼5 K), using laser-based angle-resolved photoemission spectroscopy. Whereas the previously discovered high-T_{c} superconductors such as copper oxides and iron-based superconductors, which are believed to have unconventional superconducting mechanisms, have 3d electrons in their conduction bands, the conduction band of BiS_{2}-based superconductors mainly consists of Bi 6p electrons, and, hence, the conventional superconducting mechanism might be expected. Contrary to this expectation, we observe a strongly anisotropic superconducting gap. This result strongly suggests that the pairing mechanism for NdO_{0.71}F_{0.29}BiS_{2} is an unconventional one and we attribute the observed anisotropy to competitive or cooperative multiple paring interactions.

Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis.

Proteins Rpf2 and Rrs1 are required for 60S ribosomal subunit maturation. These proteins are necessary for the recruitment of three ribosomal components (5S ribosomal RNA [rRNA], RpL5 and RpL11) to the 90S ribosome precursor and subsequent 27SB pre-rRNA processing. Here we present the crystal structure of the Aspergillus nidulans (An) Rpf2-Rrs1 core complex. The core complex contains the tightly interlocked N-terminal domains of Rpf2 and Rrs1. The Rpf2 N-terminal domain includes a Brix domain characterized by similar N- and C-terminal architecture. The long α-helix of Rrs1 joins the C-terminal half of the Brix domain as if it were part of a single molecule. The conserved proline-rich linker connecting the N- and C-terminal domains of Rrs1 wrap around the side of Rpf2 and anchor the C-terminal domain of Rrs1 to a specific site on Rpf2. In addition, gel shift analysis revealed that the Rpf2-Rrs1 complex binds directly to 5S rRNA. Further analysis of Rpf2-Rrs1 mutants demonstrated that Saccharomyces cerevisiae Rpf2 R236 (corresponds to R238 of AnRpf2) plays a significant role in this binding. Based on these studies and previous reports, we have proposed a model for ribosomal component recruitment to the 90S ribosome precursor.

Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea.

Methanogenic archaea lack cysteinyl-tRNA synthetase; they synthesize Cys-tRNA and cysteine in a tRNA-dependent manner. Two enzymes are required: Phosphoseryl-tRNA synthetase (SepRS) forms phosphoseryl-tRNA(Cys) (Sep-tRNA(Cys)), which is converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS). This represents the ancestral pathway of Cys biosynthesis and coding in archaea. Here we report a translation factor, SepCysE, essential for methanococcal Cys biosynthesis; its deletion in Methanococcus maripaludis causes Cys auxotrophy. SepCysE acts as a scaffold for SepRS and SepCysS to form a stable high-affinity complex for tRNA(Cys) causing a 14-fold increase in the initial rate of Cys-tRNA(Cys) formation. Based on our crystal structure (2.8-Šresolution) of a SepCysS⋅SepCysE complex, a SepRS⋅SepCysE⋅SepCysS structure model suggests that this ternary complex enables substrate channeling of Sep-tRNA(Cys). A phylogenetic analysis suggests coevolution of SepCysE with SepRS and SepCysS in the last universal common ancestral state. Our findings suggest that the tRNA-dependent Cys biosynthesis proceeds in a multienzyme complex without release of the intermediate and this mechanism may have facilitated the addition of Cys to the genetic code.

Anharmonicity in the High-Temperature Cmcm Phase of SnSe: Soft Modes and Three-Phonon Interactions.

The layered semiconductor SnSe is one of the highest-performing thermoelectric materials known. We demonstrate, through a first-principles lattice-dynamics study, that the high-temperature Cmcm phase is a dynamic average over lower-symmetry minima separated by very small energetic barriers. Compared to the low-temperature Pnma phase, the Cmcm phase displays a phonon softening and enhanced three-phonon scattering, leading to an anharmonic damping of the low-frequency modes and hence the thermal transport. We develop a renormalization scheme to quantify the effect of the soft modes on the calculated properties, and confirm that the anharmonicity is an inherent feature of the Cmcm phase. These results suggest a design concept for thermal insulators and thermoelectric materials, based on displacive instabilities, and highlight the power of lattice-dynamics calculations for materials characterization.

Dual-Energy Spectral CT: Various Clinical Vascular Applications.

Single-source dual-energy (DE) computed tomography (CT) with fast switching of tube voltage allows projection-based image reconstruction, substantial reduction of beam-hardening effects, reconstruction of accurate monochromatic images and material decomposition images (MDIs), and detailing of material composition by using x-ray spectral information. In vascular applications, DE CT is expected to overcome limitations of standard single-energy CT angiography, including patient exposure to nephrotoxic contrast medium and carcinogenic radiation, insufficient contrast vascular enhancement, interference from metallic and beam-hardening artifacts and severe vessel calcification, and limited tissue characterization and perfusion assessment. Acquisition of low-energy monochromatic images and iodine/water MDIs can reasonably reduce contrast agent dose and improve vessel enhancement. Acquisition of virtual noncontrast images, such as water/iodine MDIs, can reduce overall radiation exposure by replacing true noncontrast CT in each examination. Acquisition of monochromatic images by using metal artifact reduction software or acquisition of iodine/water MDIs can reduce metal artifacts with preserved or increased vessel contrast, and subtraction of monochromatic images between two energy levels can subtract coils composed of dense metallic materials. Acquisition of iodine/calcium (ie, hydroxyapatite) MDIs permits subtraction of vessel calcification and improves vessel lumen delineation. Sensitive detection of lipid-rich plaque can be achieved by using fat/water MDIs, the spectral Hounsfield unit curve (energy level vs CT attenuation), and a histogram of effective atomic numbers included in an image. Various MDIs are useful for accurate differentiation among materials with high attenuation values, including contrast medium, calcification, and fresh hematoma. Iodine/water MDIs are used to assess organ perfusion, such as in the lungs and myocardium. Understanding these DE CT techniques enhances the value of CT for vascular applications. (©)RSNA, 2016.

Structural basis of reverse nucleotide polymerization.

Nucleotide polymerization proceeds in the forward (5'-3') direction. This tenet of the central dogma of molecular biology is found in diverse processes including transcription, reverse transcription, DNA replication, and even in lagging strand synthesis where reverse polymerization (3'-5') would present a "simpler" solution. Interestingly, reverse (3'-5') nucleotide addition is catalyzed by the tRNA maturation enzyme tRNA(His) guanylyltransferase, a structural homolog of canonical forward polymerases. We present a Candida albicans tRNA(His) guanylyltransferase-tRNA(His) complex structure that reveals the structural basis of reverse polymerization. The directionality of nucleotide polymerization is determined by the orientation of approach of the nucleotide substrate. The tRNA substrate enters the enzyme's active site from the opposite direction (180° flip) compared with similar nucleotide substrates of canonical 5'-3' polymerases, and the finger domains are on opposing sides of the core palm domain. Structural, biochemical, and phylogenetic data indicate that reverse polymerization appeared early in evolution and resembles a mirror image of the forward process.

Structural change in FtsZ Induced by intermolecular interactions between bound GTP and the T7 loop.

FtsZ is a prokaryotic homolog of tubulin and is a key molecule in bacterial cell division. FtsZ with bound GTP polymerizes into tubulin-like protofilaments. Upon polymerization, the T7 loop of one subunit is inserted into the nucleotide-binding pocket of the second subunit, which results in GTP hydrolysis. Thus, the T7 loop is important for both polymerization and hydrolysis in the tubulin/FtsZ family. Although x-ray crystallography revealed both straight and curved conformations of tubulin, only a curved structure was known for FtsZ. Recently, however, FtsZ from Staphylococcus aureus has been shown to have a very different conformation from the canonical FtsZ structure. The present study was performed to investigate the structure of FtsZ from Staphylococcus aureus by mutagenesis experiments; the effects of amino acid changes in the T7 loop on the structure as well as on GTPase activity were studied. These analyses indicated that FtsZ changes its conformation suitable for polymerization and GTP hydrolysis by movement between N- and C-subdomains via intermolecular interactions between bound nucleotide and residues in the T7 loop.

Prediction of Low-Thermal-Conductivity Compounds with First-Principles Anharmonic Lattice-Dynamics Calculations and Bayesian Optimization.

Compounds of low lattice thermal conductivity (LTC) are essential for seeking thermoelectric materials with high conversion efficiency. Some strategies have been used to decrease LTC. However, such trials have yielded successes only within a limited exploration space. Here, we report the virtual screening of a library containing 54,779 compounds. Our strategy is to search the library through Bayesian optimization using for the initial data the LTC obtained from first-principles anharmonic lattice-dynamics calculations for a set of 101 compounds. We discovered 221 materials with very low LTC. Two of them even have an electronic band gap <1 eV, which makes them exceptional candidates for thermoelectric applications. In addition to those newly discovered thermoelectric materials, the present strategy is believed to be powerful for many other applications in which the chemistry of materials is required to be optimized.

Current and Novel Imaging Techniques in Coronary CT.

Multidetector coronary computed tomography (CT), which is widely performed to assess coronary artery disease noninvasively and accurately, provides excellent image quality. Use of electrocardiography (ECG)-controlled tube current modulation and low tube voltage can reduce patient exposure to nephrotoxic contrast media and carcinogenic radiation when using standard coronary CT with a retrospective ECG-gated helical scan. Various imaging techniques are expected to overcome the limitations of standard coronary CT, which also include insufficient spatial and temporal resolution, beam-hardening artifacts, limited coronary plaque characterization, and an inability to allow functional assessment of coronary stenosis. Use of a step-and-shoot scan, iterative reconstruction, and a high-pitch dual-source helical scan can further reduce radiation dose. Dual-energy CT can improve contrast medium enhancement and reasonably reduce the contrast dose when combined with noise reduction with the use of iterative reconstruction. High-definition CT can improve spatial resolution and diagnostic evaluation of small or peripheral coronary vessels and coronary stents. Dual-source CT and a motion correction algorithm can improve temporal resolution and reduce coronary motion artifacts. Whole-heart coverage with 320-detector CT and an intelligent boundary registration algorithm can eliminate stair-step artifacts. By decreasing beam hardening and enabling material decomposition, dual-energy CT is expected to remove or reduce the depiction of coronary calcification to improve intraluminal evaluation of calcified vessels and to provide detailed analysis of coronary plaque components and accurate qualitative and quantitative assessment of myocardial perfusion. Fractional flow reserve derived from coronary CT is a state-of-the-art noninvasive technique for accurately identifying myocardial ischemia beyond coronary CT. Understanding these techniques is important to enhance the value of coronary CT for assessment of coronary artery disease.