42 research outputs found

    Temperature-dependent spin polarization of Heusler Co2MnSi from the disordered local-moment approach : effects of atomic disordering and nonstoichiometry

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    Half-metallic ferromagnets have been widely investigated by first-principles density-functional theory (DFT) calculations, but extending such studies to investigate spin-polarization at finite temperatures is still challenging due to the difficulty of incorporating temperature effects appropriately. We present DFT calculations, based on a Green's function formulation, which include thermal effects via the disordered local-moment method to address this issue. The calculations are carried out for Heusler Co2MnSi alloys in order to investigate the temperature dependence of spin polarization, where atomic-disordering and nonstoichiometric effects are taken into account. Our results show that the spin polarization strongly depends on temperature and that a Co d-orbital effect plays a key role in this effect. Furthermore, we find that the temperature-dependent spin polarization of Co2MnSi can be improved by reducing the Co content and incorporating extra Mn

    A Comprehensive Sequence and Disease Correlation Analyses for the C-Terminal Region of CagA Protein of Helicobacter pylori

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    Chronic Helicobacter pylori infection is known to be associated with the development of peptic ulcer, gastric cancer and gastric lymphoma. Currently, the bacterial factors of H. pylori are reported to be important in the development of gastroduodenal diseases. CagA protein, encoded by the cagA, is the best studied virulence factor of H. pylori. The pathogenic CagA protein contains a highly polymorphic Glu-Pro-Ile-Tyr-Ala (EPIYA) repeat region in the C-terminal. This repeat region is reported to be involved in the pathogenesis of gastroduodenal diseases. The segments containing EPIYA motifs have been designated as segments A, B, C, and D; however the classification and disease relation are still unclear. This study used 560 unique CagA sequences containing 1,796 EPIYA motifs collected from public resources, including 274 Western and 286 East Asian strains with clinical data obtained from 433 entries. Fifteen types of EPIYA or EPIYA-like sequences are defined. In addition to four previously reported major segment types, several minor segment types (e.g., segment B′, B′′) and more than 30 sequence types (e.g., ABC, ABD) were defined using our classification method. We confirm that the sequences from Western and East Asian strains contain segment C and D, respectively. We also confirm that strains with two EPIYA segment C have a greater chance of developing gastric cancer than those with one segment C. Our results shed light on the relationships between the types of CagAs, the country of origin of each sequence type, and the frequency of gastric disease

    Confinement, chiral symmetry, and the lattice

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    Two crucial properties of QCD, confinement and chiral symmetry breaking, cannot be understood within the context of conventional Feynman perturbation theory. Non-perturbative phenomena enter the theory in a fundamental way at both the classical and quantum level. Over the years a coherent qualitative picture of the interplay between chiral symmetry, quantum mechanical anomalies, and the lattice has emerged and is reviewed here.Comment: 126 pages, 36 figures. Revision corrects additional typos and renumbers equations to be more consistent with the published versio

    The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

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    The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations

    The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

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    Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics
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