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, $\lambda$ (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

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

Challenges of Religious Literacy in Education : Islam and the Governance of Religious Diversity in Multi-faith Schools

This chapter seeks take part in an emerging research where religion is approached as a whole school endeavor. Previous research and policy recommendations typically focused on teaching about religion in school, but the accommodation of religious diversity in the wider school culture merits more attention. Based on observations in our multiple case studies, we discuss the multi-level governance of religious diversity in Finnish multi-faith schools with a particular focus on the challenges of religious literacy for educators. The three examples we present focus on the inclusion of Muslims in Finnish schools and in particular on the challenges for educator (1) in interpreting the distinction between religion and culture, (2) in recognizing and handling intra-religious diversity, and (3) in being aware of Protestant conceptions of religion and culture. A theme cutting across these examples is how they reflect the tendencies either to see different situations merely through the lens of religion (religionisation), or not to recognize the importance of religion at all (religion-blindness). We argue that religious literacy should be recognized and developed as a vital part of the intercultural competencies of educators.Peer reviewe