Normal Mode Determination of Perovskite Crystal Structures with Octahedral Rotations: Theory and Applications

Nuclear site analysis methods are used to enumerate the normal modes of $ABX_{3}$ perovskite polymorphs with octahedral rotations. We provide the modes of the fourteen subgroups of the cubic aristotype describing the Glazer octahedral tilt patterns, which are obtained from rotations of the $BX_{6}$ octahedra with different sense and amplitude about high symmetry axes. We tabulate all normal modes of each tilt system and specify the contribution of each atomic species to the mode displacement pattern, elucidating the physical meaning of the symmetry unique modes. We have systematically generated 705 schematic atomic displacement patterns for the normal modes of all 15 (14 rotated + 1 unrotated) Glazer tilt systems. We show through some illustrative examples how to use these tables to identify the octahedral rotations, symmetric breathing, and first-order Jahn-Teller anti-symmetric breathing distortions of the $BX_{6}$ octahedra, and the associated Raman selection rules. We anticipate that these tables and schematics will be useful in understanding the lattice dynamics of bulk perovskites and would serve as reference point in elucidating the atomic origin of a wide range of physical properties in synthetic perovskite thin films and superlattices.Comment: 17 pages, 3 figures, 17 tables. Supporting information accessed through link specified within manuscrip

Fungal dysbiosis predicts the diagnosis of pediatric Crohn's disease

AIM: To investigate the accuracy of fungal dysbiosis in mucosa and stool for predicting the diagnosis of Crohn’s disease (CD). METHODS: Children were prospectively enrolled in two medical centers: one university hospital and one private gastroenterology clinic in the city of Riyadh, Kingdom of Saudi Arabia. The children with confirmed diagnosis of CD by standard guidelines were considered cases, and the others were considered non-inflammatory bowel disease controls. Mucosal and stool samples were sequenced utilizing Illumina MiSeq chemistry following the manufacturer’s protocols, and abundance and diversity of fungal taxa in mucosa and stool were analyzed. Sparse logistic regression was used to predict the diagnosis of CD. The accuracy of the classifier was tested by computing the receiver operating characteristic curves with 5-fold stratified cross-validation under 100 permutations of the training data partition and the mean area under the curve (AUC) was calculated. RESULTS: All the children were Saudi nationals. There were 15 children with CD and 20 controls. The mean age was 13.9 (range: 6.7-17.8) years for CD children and 13.9 (3.25-18.6) years for controls, and 10/15 (67%) of the CD and 13/20 (65%) of the control subjects were boys. CD locations at diagnosis were ileal (L1) in 4 and colonic (L3) in 11 children, while CD behavior was non-stricturing and non-penetrating (B1) in 12 and stricturing (B2) in 3 children. The mean AUC for the fungal dysbiosis classifier was significantly higher in stools (AUC = 0.85 ± 0.057) than in mucosa (AUC = 0.71 ± 0.067) (P < 0.001). Most fungal species were significantly more depleted in stools than mucosal samples, except for Saccharomyces cerevisiae and S. bayanus, which were significantly more abundant. Diversity was significantly more reduced in stools than in mucosa. CONCLUSION: We found high AUC of fungal dysbiosis in fecal samples of children with CD, suggesting high accuracy in predicting diagnosis of CD. Key Words: Fungiome, Mycobiome, Crohn’s disease, Inflammation, Saudi children Core tip: We found high accuracy of fungal dysbiosis in predicting diagnosis of Crohn’s disease (CD), a finding similar to bacterial dysbiosis. However, the higher area under the curve for the fungal dysbiosis classifier in stool (0.85 ± 0.057) than in mucosa (0.71 ± 0.067) (P < 0.001), contrasts with bacterial studies, suggesting higher accuracy of stool samples. Although the clinical application of this finding is limited at present by the high cost of fungal analysis, such information is important from a scientific viewpoint, to increase the understanding of the role of fungal flora in CD and to stimulate further studies.The authors extend their appreciations to the Deanship of Scientific Research at King Saud University in Riyadh, Kingdom of Saudi Arabia for funding this work through Research Group No [RGP-1436-007]. This work was also supported by a grant from the Simons Foundation [No. 409704] to Kirill Korolev) and by the startup fund from Boston University to Kirill Korolev. Simulations were carried out on Shared Computing Cluster at Boston University. Rajita Menon was partially supported by a Hariri Graduate Fellowship from Boston University. Harland Winter, MD received support from Martin Schlaff and the Diane and Dorothy Brooks Foundation. (RGP-1436-007 - King Saud University in Riyadh, Kingdom of Saudi Arabia; 409704 - Simons Foundation; Boston University; Hariri Graduate Fellowship from Boston University; Diane and Dorothy Brooks Foundation)Published versio

Ancient technology and punctuated change: Detecting the emergence of the Edomite Kingdom in the Southern Levant.

While the punctuated equilibrium model has been employed in paleontological and archaeological research, it has rarely been applied for technological and social evolution in the Holocene. Using metallurgical technologies from the Wadi Arabah (Jordan/Israel) as a case study, we demonstrate a gradual technological development (13th-10th c. BCE) followed by a human agency-triggered punctuated "leap" (late-10th c. BCE) simultaneously across the entire region (an area of ~2000 km2). Here, we present an unparalleled, diachronic archaeometallurgical dataset focusing on elemental analysis of dozens of well-dated slag samples. Based on the results, we suggest punctuated equilibrium provides an innovative theoretical model for exploring ancient technological changes in relation to larger sociopolitical conditions-in the case at hand the emergence of biblical Edom-, exemplifying its potential for more general cross-cultural applications

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations. Results We reconstructed the stoichiometric matrix of S. coelicolor, including the major antibiotic biosynthesis pathways, and performed flux balance analysis to predict flux changes that occur when the cell switches from biomass to antibiotic production. We defined the model input based on observed fermenter culture data and used a dynamically varying objective function to represent the metabolic switch. The predicted fluxes of many genes show highly significant correlation to the time series of the corresponding gene expression data. Individual mispredictions identify novel links between antibiotic production and primary metabolism. Conclusion Our results show the usefulness of constraint-based modeling for providing a detailed interpretation of time course gene expression data

Wave function-dependent mobility and suppression of interface roughness scattering in a strained SiGe p-channel field-effect structure

The 4 K Hall mobility has been measured in a top-gated, inverted, modulation-doped Si/Si0.8Ge0.2 structure having a Si:B doping layer beneath the alloy. From comparisons with theoretical calculations, we argue that, unlike an ordinary enhancement-mode SiGe p-channel metal–oxide–semiconductor structure, this configuration leads to a decrease of interface roughness scattering with increasing sheet carrier density. We also speculate on the nature of the interface charge observed in these structures at low temperature