7 research outputs found

    Information entropy and nucleon correlations in nuclei

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    The information entropies in coordinate and momentum spaces and their sum (SrS_r, SkS_k, SS) are evaluated for many nuclei using "experimental" densities or/and momentum distributions. The results are compared with the harmonic oscillator model and with the short-range correlated distributions. It is found that SrS_r depends strongly on lnA\ln A and does not depend very much on the model. The behaviour of SkS_k is opposite. The various cases we consider can be classified according to either the quantity of the experimental data we use or by the values of SS, i.e., the increase of the quality of the density and of the momentum distributions leads to an increase of the values of SS. In all cases, apart from the linear relation S=a+blnAS=a+b\ln A, the linear relation S=aV+bVlnVS=a_V+b_V \ln V also holds. V is the mean volume of the nucleus. If SS is considered as an ensemble entropy, a relation between AA or VV and the ensemble volume can be found. Finally, comparing different electron scattering experiments for the same nucleus, it is found that the larger the momentum transfer ranges, the larger the information entropy is. It is concluded that SS could be used to compare different experiments for the same nucleus and to choose the most reliable one.Comment: 14 pages, 4 figures, 2 table

    Nuclear symmetry energy effects on neutron stars properties

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    We construct a class of nuclear equations of state based on a schematic potential model, that originates from the work of Prakash et. al. \cite{Prakash-88}, which reproduce the results of most microscopic calculations. The equations of state are used as input for solving the Tolman-Oppenheimer-Volkov equations for corresponding neutron stars. The potential part contribution of the symmetry energy to the total energy is parameterized in a generalized form both for low and high values of the baryon density. Special attention is devoted to the construction of the symmetry energy in order to reproduce the results of most microscopic calculations of dense nuclear matter. The obtained nuclear equations of state are applied for the systematic study of the global properties of a neutron star (masses, radii and composition). The calculated masses and radii of the neutron stars are plotted as a function of the potential part parameters of the symmetry energy. A linear relation between these parameters, the radius and the maximum mass of the neutron star is obtained. In addition, a linear relation between the radius and the derivative of the symmetry energy near the saturation density is found. We also address on the problem of the existence of correlation between the pressure near the saturation density and the radius.Comment: 17 pages, 25 figure

    Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

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    We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term “the expanding mobility model.” Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3_3-based genetic distances, but not by the commonly used FST_{ST} statistic, due to the sensitivity of FST_{ST}, but not outgroup-f3_3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene

    Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

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    BACKGROUND: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. RESULTS: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. CONCLUSIONS: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia

    Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system

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    The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time. © 2018 Elsevier Inc

    Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

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    We preŞent a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of com-plex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 preŞent-day published genomes, we found that genetic diversity within each region steadily increased through the Holo-cene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holo-cene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term the expanding mobility model.Interestingly, this increase in in-ter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the Şensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.Wenner-Gren Foundation Dissertation Fieldwork grant; H2020 ERC Consolidator grant; EMBO Scientific Exchange grant [9573]; H2020-WIDESPREAD-05-2020 TWINNING grant [772390 NEOGENE]; TUBITAK of Turkey [8883]; Klaus-Tschira Foundation [952317 NEOMATRIX]; German Research Foundation (DFG) [117Z229]; National Genomics Infrastructure in Stockholm - Science for Life Laboratory; Knut and Alice Wallenberg Foundation [SCHA 889/4-4]; Swedish Research Council; SNIC/Uppsala Multidisciplinary Center for Advanced Computational (UPPMAX) projects; operational programme Competitiveness, Entrepreneurship and Innovation (NSRF 2014-2020); European Union (European Regional Development Fund) [uppstore20180102, SNIC 2018/8-293, SNIC 2018/8-88, SNIC 2021-2-17]; Hacettepe University Scientific Research Projects Coordination Unit [MIS 5002735, MIS 5002478]; [16769]; [14528]We thank Orhan Efe Yavuz, Anna-Sapfo Malaspinas, Flora Jay, Ayshin Ghali-chi, Yesxim Ayd?n Son, Can Alkan, HamitIzgi, Asl?han Ilgaz, Maja Krzewinska, and all colleagues at the METU CompEvo, Hacettepe Human_G and Center for Palaeogenetics (CPG) for their support, suggestions, and/or comments. We also thank three anonymous reviewers for their constructive criticism. The authors acknowledge support from Wenner-Gren Foundation Dissertation Fieldwork grant (no. 9573 to D. Koptekin); H2020 ERC Consolidator grant (no. 772390 NEOGENE to M.S.); EMBO Scientific Exchange grant (no. 8883 to D. Koptekin); H2020-WIDESPREAD-05-2020 TWINNING grant (no. 952317 NEOMATRIX to M.S.); TUBITAK of Turkey (no. 117Z229 to M.S.); Klaus-Tschira Foundation; German Research Foundation (DFG, grant no. SCHA 889/4-4 to A. Schachner); the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, and the Swedish Research Council; SNIC/Uppsala Multidisciplinary Center for Advanced Computational (UPPMAX) projects uppstore20180102, SNIC 2018/8-293, SNIC 2018/8-88, and SNIC 2021-2-17; the projects HELLAS-CH (MIS 5002735), implemented under Action for Strengthening Research and Innovation Infrastructures, and POLITEIA-II (MIS 5002478), implemented under Action for the Strategic Development on the Research and Technological Sector, both funded by the operational programme Competitiveness, Entrepreneurship and Innovation (NSRF 2014-2020) and co-financed by Greece and the European Union (European Regional Development Fund); and Hacettepe University Scientific Research Projects Coordination Unit (nos. 16769 and 14528 to A.M.B.). Computations were performed at NEOGENE (Middle East Technical University) and UPPMAX resources

    Type VII secretion systems: structure, functions and transport models

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