278 research outputs found
Monte Carlo simulations of 2d hard core lattice gases
Monte Carlo simulations are used to study lattice gases of particles with
extended hard cores on a two dimensional square lattice. Exclusions of one and
up to five nearest neighbors (NN) are considered. These can be mapped onto hard
squares of varying side length, (in lattice units), tilted by some
angle with respect to the original lattice. In agreement with earlier studies,
the 1NN exclusion undergoes a continuous order-disorder transition in the Ising
universality class. Surprisingly, we find that the lattice gas with exclusions
of up to second nearest neighbors (2NN) also undergoes a continuous phase
transition in the Ising universality class, while the Landau-Lifshitz theory
predicts that this transition should be in the universality class of the XY
model with cubic anisotropy. The lattice gas of 3NN exclusions is found to
undergo a discontinuous order-disorder transition, in agreement with the
earlier transfer matrix calculations and the Landau-Lifshitz theory. On the
other hand, the gas of 4NN exclusions once again exhibits a continuous phase
transition in the Ising universality class -- contradicting the predictions of
the Landau-Lifshitz theory. Finally, the lattice gas of 5NN exclusions is found
to undergo a discontinuous phase transition.Comment: 13 pages, lots of figure
Increased p-type conductivity in GaNxSb1−x, experimental and theoretical aspects
The large increase in the p-type conductivity observed when nitrogen is added to GaSb has been studied using positron annihilation spectroscopy and ab initio calculations. Doppler broadening measurements have been conducted on samples of GaN x Sb 1− x layers grown by molecular beam epitaxy, and the results have been compared with calculated first-principle results corresponding to different defect structures. From the calculated data, binding energies for nitrogen-related defects have also been estimated. Based on the results, the increase in residual hole concentration is explained by an increase in the fraction of negative acceptor-type defects in the material. As the band gap decreases with increasing N concentration, the ionization levels of the defects move closer to the valence band. Ga vacancy-type defects are found to act as positron trapping defects in the material, and the ratio of Ga vacancy-type defects to Ga antisites is found to be higher than that of the p-type bulk GaSb substrate. Beside Ga vacancies, the calculated results imply that complexes of a Ga vacancy and nitrogen could be present in the material
Mutation accumulation opposes polymorphism : supergenes and the curious case of balanced lethals
Supergenes offer spectacular examples of long-term balancing selection in nature, but their origin and maintenance remain a mystery. Reduced recombination between arrangements, a critical aspect of many supergenes, protects adaptive multi-trait phenotypes but can lead to mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One outcome is the formation of maladaptive balanced lethal systems, where only heterozygotes remain viable and reproduce. We investigated the conditions under which these different outcomes occur, assuming a scenario of introgression after divergence. We found that AOD aided the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism was easily destabilized by further mutation accumulation, which was often asymmetric, disrupting the quasi-equilibrium state. Mechanisms that accelerated degeneration tended to amplify asymmetric mutation accumulation between the supergene arrangements and vice-versa. As the evolution of balanced lethal systems requires symmetric degeneration of both arrangements, this leaves only restricted conditions for their evolution, namely small population sizes and low rates of gene conversion. The dichotomy between the persistence of polymorphism and degeneration of supergene arrangements likely underlies the rarity of balanced lethal systems in nature
Targeted long-read sequencing of a locus under long-term balancing selection in Capsella
YesRapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7×10−5. A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach.This study was supported by a grant from the Swedish Research Council to T.S
Phenomenological model for the remanent magnetization of dilute quasi-one-dimensional antiferromagnets
We present a phenomenological model for the remanent magnetization at low
temperatures in the quasi-one-dimensional dilute antiferromagnets
CH_{3}NH_{3}Mn_{1-x}Cd_{x} Cl_{3}\cdot 2H_{2}O and
(CH_{3})_{2}NH_{2}Mn_{1-x}Cd_{x}Cl_{3}\cdot 2H_{2}O. The model assumes the
existence of uncompensated magnetic moments induced in the odd-sized segments
generated along the Mn(^{2+}) chains upon dilution. These moments are further
assumed to correlate ferromagnetically after removal of a cooling field. Using
a (mean-field) linear-chain approximation and reasonable set of model
parameters, we are able to reproduce the approximate linear temperature
dependence observed for the remanent magnetization in the real compounds.Comment: 5 pages, 2 figures; final version to appear in Physical Review
Fluctuating selection models and Mcdonald-Kreitman type analyses
It is likely that the strength of selection acting upon a mutation varies through time due to changes in the environment. However, most population genetic theory assumes that the strength of selection remains constant. Here we investigate the consequences of fluctuating selection pressures on the quantification of adaptive evolution using McDonald-Kreitman (MK) style approaches. In agreement with previous work, we show that fluctuating selection can generate evidence of adaptive evolution even when the expected strength of selection on a mutation is zero. However, we also find that the mutations, which contribute to both polymorphism and divergence tend, on average, to be positively selected during their lifetime, under fluctuating selection models. This is because mutations that fluctuate, by chance, to positive selected values, tend to reach higher frequencies in the population than those that fluctuate towards negative values. Hence the evidence of positive adaptive evolution detected under a fluctuating selection model by MK type approaches is genuine since fixed mutations tend to be advantageous on average during their lifetime. Never-the-less we show that methods tend to underestimate the rate of adaptive evolution when selection fluctuates
Critical behavior of 2 and 3 dimensional ferro- and antiferromagnetic spin ice systems in the framework of the Effective Field Renormalization Group technique
In this work we generalize and subsequently apply the Effective Field
Renormalization Group technique to the problem of ferro- and
antiferromagnetically coupled Ising spins with local anisotropy axes in
geometrically frustrated geometries (kagome and pyrochlore lattices). In this
framework, we calculate the various ground states of these systems and the
corresponding critical points. Excellent agreement is found with exact and
Monte Carlo results. The effects of frustration are discussed. As pointed out
by other authors, it turns out that the spin ice model can be exactly mapped to
the standard Ising model but with effective interactions of the opposite sign
to those in the original Hamiltonian. Therefore, the ferromagnetic spin ice is
frustrated, and does not order. Antiferromagnetic spin ice (in both 2 and 3
dimensions), is found to undergo a transition to a long range ordered state.
The thermal and magnetic critical exponents for this transition are calculated.
It is found that the thermal exponent is that of the Ising universality class,
whereas the magnetic critical exponent is different, as expected from the fact
that the Zeeman term has a different symmetry in these systems. In addition,
the recently introduced Generalized Constant Coupling method is also applied to
the calculation of the critical points and ground state configurations. Again,
a very good agreement is found with both exact, Monte Carlo, and
renormalization group calculations for the critical points. Incidentally, we
show that the generalized constant coupling approach can be regarded as the
lowest order limit of the EFRG technique, in which correlations outside a
frustrated unit are neglected, and scaling is substituted by strict equality of
the thermodynamic quantities.Comment: 28 pages, 9 figures, RevTeX 4 Some minor changes in the conclussions.
One reference adde
Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis
Recent results from Drosophila suggest that positive selection has a substantial impact on genomic patterns of polymorphism and divergence. However, species with smaller population sizes and/or stronger population structure may not be expected to exhibit Drosophila-like patterns of sequence variation. We test this prediction and identify determinants of levels of polymorphism and rates of protein evolution using genomic data from Arabidopsis thaliana and the recently sequenced Arabidopsis lyrata genome. We find that, in contrast to Drosophila, there is no negative relationship between nonsynonymous divergence and silent polymorphism at any spatial scale examined. Instead, synonymous divergence is a major predictor of silent polymorphism, which suggests variation in mutation rate as the main determinant of silent variation. Variation in rates of protein divergence is mainly correlated with gene expression level and breadth, consistent with results for a broad range of taxa, and map-based estimates of recombination rate are only weakly correlated with nonsynonymous divergence. Variation in mutation rates and the strength of purifying selection seem to be major drivers of patterns of polymorphism and divergence in Arabidopsis. Nevertheless, a model allowing for varying negative and positive selection by functional gene category explains the data better than a homogeneous model, implying the action of positive selection on a subset of genes. Genes involved in disease resistance and abiotic stress display high proportions of adaptive substitution. Our results are important for a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence
Causal assessment of smoking and tooth loss: A systematic review of observational studies
<p>Abstract</p> <p>Background</p> <p>Tooth loss impairs oral function. The aim of the present review was to evaluate the causal association between smoking and tooth loss on the basis of high-quality studies.</p> <p>Methods</p> <p>Relevant literature was searched and screened, and the methodological quality was assessed. Information on the strength of the association between smoking and tooth loss, the dose-response relationship and natural experimental data was collected and evaluated with respect to consistency and study design.</p> <p>Results</p> <p>Our literature search yielded 496 citations, and 6 cross-sectional and 2 cohort high-quality studies examining 58,755 subjects in four countries. All studies reported significant associations, although the strength of the association was usually moderate. Four studies reported dose-response relationships between exposure to smoking and the risk of developing tooth loss. A decrease in the risk of tooth loss for former smokers was evident in six studies. Interpretation of evidence for each element was consistent, despite some shortcomings regarding study type and population.</p> <p>Conclusions</p> <p>Based on the consistent evidence found with the existing biological plausibility, a causal association between smoking and tooth loss is highly likely. Further studies using a cohort design and different populations are necessary to confirm this association.</p
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