Non-deterministic density classification with diffusive probabilistic cellular automata

We present a probabilistic cellular automaton (CA) with two absorbing states which performs classification of binary strings in a non-deterministic sense. In a system evolving under this CA rule, empty sites become occupied with a probability proportional to the number of occupied sites in the neighborhood, while occupied sites become empty with a probability proportional to the number of empty sites in the neighborhood. The probability that all sites become eventually occupied is equal to the density of occupied sites in the initial string.Comment: 4 pages, 4 figure

Renormalized Equilibria of a Schloegl Model Lattice Gas

A lattice gas model for Schloegl's second chemical reaction is described and analyzed. Because the lattice gas does not obey a semi-detailed-balance condition, the equilibria are non-Gibbsian. In spite of this, a self-consistent set of equations for the exact homogeneous equilibria are described, using a generalized cluster-expansion scheme. These equations are solved in the two-particle BBGKY approximation, and the results are compared to numerical experiment. It is found that this approximation describes the equilibria far more accurately than the Boltzmann approximation. It is also found, however, that spurious solutions to the equilibrium equations appear which can only be removed by including effects due to three-particle correlations.Comment: 21 pages, REVTe

Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes.

Understanding how phenotypic differences between males and females arise from the sex-biased expression of nearly identical genomes can reveal important insights into the biology and evolution of a species. Among Anopheles mosquito species, these phenotypic differences include vectorial capacity, as it is only females that blood feed and thus transmit human malaria. Here, we use RNA-seq data from multiple tissues of four vector species spanning the Anopheles phylogeny to explore the genomic and evolutionary properties of sex-biased genes. We find that, in these mosquitoes, in contrast to what has been found in many other organisms, female-biased genes are more rapidly evolving in sequence, expression, and genic turnover than male-biased genes. Our results suggest that this atypical pattern may be due to the combination of sex-specific life history challenges encountered by females, such as blood feeding. Furthermore, female propensity to mate only once in nature in male swarms likely diminishes sexual selection of post-reproductive traits related to sperm competition among males. We also develop a comparative framework to systematically explore tissue- and sex-specific splicing to document its conservation throughout the genus and identify a set of candidate genes for future functional analyses of sex-specific isoform usage. Finally, our data reveal that the deficit of male-biased genes on the X Chromosomes in Anopheles is a conserved feature in this genus and can be directly attributed to chromosome-wide transcriptional regulation that de-masculinizes the X in male reproductive tissues

Adaptive Gene Expression Divergence Inferred from Population Genomics

Detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. Genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression evolution. Here, we combined genomic expression data—analyzed in a phylogenetic context—with whole genome light-shotgun sequence data from six Drosophila simulans lines and reference sequences from D. melanogaster and D. yakuba. These data allowed us to use molecular population genetics to test for neutral versus adaptive gene expression divergence on a genomic scale. We identified recent and recurrent adaptive evolution along the D. simulans lineage by contrasting sequence polymorphism within D. simulans to divergence from D. melanogaster and D. yakuba. Genes that evolved higher levels of expression in D. simulans have experienced adaptive evolution of the associated 3′ flanking and amino acid sequence. Concomitantly, these genes are also decelerating in their rates of protein evolution, which is in agreement with the finding that highly expressed genes evolve slowly. Interestingly, adaptive evolution in 5′ cis-regulatory regions did not correspond strongly with expression evolution. Our results provide a genomic view of the intimate link between selection acting on a phenotype and associated genic evolution

Embedded Mean-Field Theory for Solution-Phase Transition-Metal Polyolefin Catalysis

Decreasing the wall-clock time of quantum mechanics/molecular mechanics (QM/MM) calculations without sacrificing accuracy is a crucial prerequisite for widespread simulation of solution-phase dynamical processes. In this work, we demonstrate the use of embedded mean-field theory (EMFT) as the QM engine in QM/MM molecular dynamics (MD) simulations to examine polyolefin catalysts in solution. We show that employing EMFT in this mode preserves the accuracy of hybrid-functional DFT in the QM region, while providing up to 20-fold reductions in the cost per SCF cycle, thereby increasing the accessible simulation time-scales. We find that EMFT reproduces DFT-computed binding energies and optimized bond lengths to within chemical accuracy, as well as consistently ranking conformer stability. Furthermore, solution-phase EMFT/MM simulations provide insight into the interaction strength of strongly coordinating and bulky counterions

Electronic structure of wurtzite and zinc-blende AlN

The electronic structure of AlN in wurtzite and zinc-blende phases is studied experimentally and theoretically. By using x-ray emission spectroscopy, the Al 3p, Al 3s and N 2p spectral densities are obtained. The corresponding local and partial theoretical densities of states (DOS), as well as the total DOS and the band structure, are calculated by using the full potential linearized augmented plane wave method, within the framework of the density functional theory. There is a relatively good agreement between the experimental spectra and the theoretical DOS, showing a large hybridization of the valence states all along the valence band. The discrepancies between the experimental and theoretical DOS, appearing towards the high binding energies, are ascribed to an underestimation of the valence band width in the calculations. Differences between the wurtzite and zinc-blende phases are small and reflect the slight variations between the atomic arrangements of both phases

Cross-Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex.

Y chromosome function, structure and evolution is poorly understood in many species, including the Anopheles genus of mosquitoes-an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility. Here, we used an F1 × F0 crossing scheme to overcome a severe bottleneck of male hybrid incompatibilities that enabled us to experimentally purify a genetically labeled A. gambiae Y chromosome in an A. arabiensis background. Whole genome sequencing (WGS) confirmed that the A. gambiae Y retained its original sequence content in the A. arabiensis genomic background. In contrast to comparable experiments in Drosophila, we find that the presence of a heterospecific Y chromosome has no significant effect on the expression of A. arabiensis genes, and transcriptional differences can be explained almost exclusively as a direct consequence of transcripts arising from sequence elements present on the A. gambiae Y chromosome itself. We find that Y hybrids show no obvious fertility defects, and no substantial reduction in male competitiveness. Our results demonstrate that, despite their radically different structure, Y chromosomes of these two species of the gambiae complex that diverged an estimated 1.85 MYA function interchangeably, thus indicating that the Y chromosome does not harbor loci contributing to hybrid incompatibility. Therefore, Y chromosome gene flow between members of the gambiae complex is possible even at their current level of divergence. Importantly, this also suggests that malaria control interventions based on sex-distorting Y drive would be transferable, whether intentionally or contingent, between the major malaria vector species

X-ray absorption spectroscopy study of diluted magnetic semiconductors: Zn1-xMxSe (M = Mn, Fe, Co) and Zn1-xMnxY (Y = Se, Te)

We have investigated 3d electronic states of doped transition metals in II-VI diluted magnetic semiconductors, Zn1-xMxSe (M = Mn, Fe, Co) and Zn1-xMnxY (Y = Se, Te), using the transition-metal L2,3-edge X-ray absorption spectroscopy (XAS) measurements. In order to explain the XAS spectra, we employed a tetragonal cluster model calculation, which includes not only the full ionic multiplet structure but also configuration interaction (CI). The results show that CI is essential to describe the experimental spectra adequately, indicating the strong hybridization between the transition metal 3d and the ligand p orbitals. In the study of Zn1-xMnxY (Y = Se, Te), we also found considerable spectral change in the Mn L2,3-edge XAS spectra for different ligands, confirming the importance of the hybridization effects in these materials.Comment: This paper consists of 22 pages including 4 figures. This paper is submitted to Physical Review

SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes

Mosquitoes in the Anopheles gambiae complex show rapid ecological and behavioral diversification, traits that promote malaria transmission and complicate vector control efforts. A high-density, genome-wide mosquito SNP-genotyping array allowed mapping of genomic differentiation between populations and species that exhibit varying levels of reproductive isolation. Regions near centromeres or within polymorphic inversions exhibited the greatest genetic divergence, but divergence was also observed elsewhere in the genomes. Signals of natural selection within populations were overrepresented among genomic regions that are differentiated between populations, implying that differentiation is often driven by population-specific selective events. Complex genomic differentiation among speciating vector mosquito populations implies that tools for genome-wide monitoring of population structure will prove useful for the advancement of malaria eradication