Large non-adiabatic hole polarons and matrix element effects in the angle-resolved photoemission spectroscopy of dielectric cuprates

It has been made an extention of the conventional theory based on the assumption of the well isolated Zhang-Rice singlet to be a first electron-removal state in dielectric copper oxide. One assumes the photohole has been localised on either small (pseudo)Jahn-Teller polaron or large non-adiabatic polaron enclosed one or four to five $CuO_4$ centers, respectively, with active one-center valent $(^{1}A_{1g}-{}^{1,3}E_{u})$ manifold. In the framework of the cluster model we have performed a model microscopic calculation of the ${\bf k}$-dependence of the matrix element effects and photon polarization effects for the angle-resolved photoemission in dielectric cuprate like $Sr_{2}CuO_{2}Cl_{2}$. We show that effects like the ''remnant Fermi surface'' detected in ARPES experiment for $Ca_{2}CuO_{2}Cl_{2}$ may be, in fact, a reflection of the matrix element effects, not a reflection of the original band-structure Fermi surface, or the strong antiferromagnetic correlations. The measured dispersion-like features in the low-energy part of the ARPES spectra may be a manifestation of the complex momentum-dependent spectral line-shape of the large PJT polaron response, not the dispersion of the well-isolated Zhang-Rice singlet in antiferromagnetic matrix.Comment: 16 pages, TeX, 9 eps figures adde

Rate of promoter class turn-over in yeast evolution

BACKGROUND: Phylogenetic conservation at the DNA level is routinely used as evidence of molecular function, under the assumption that locations and sequences of functional DNA segments remain invariant in evolution. In particular, short DNA segments participating in initiation and regulation of transcription are often conserved between related species. However, transcription of a gene can evolve, and this evolution may involve changes of even such conservative DNA segments. Genes of yeast Saccharomyces have promoters of two classes, class 1 (TATA-containing) and class 2 (non-TATA-containing). RESULTS: Comparison of upstream non-coding regions of orthologous genes from the five species of Saccharomyces sensu stricto group shows that among 212 genes which very likely have class 1 promoters in S. cerevisiae, 17 probably have class 2 promoters in one or more other species. Conversely, among 322 genes which very likely have class 2 promoters in S. cerevisiae, 44 probably have class 1 promoters in one or more other species. Also, for at least 2 genes from the set of 212 S. cerevisiae genes with class 1 promoters, the locations of the TATA consensus sequences are substantially different between the species. CONCLUSION: Our results indicate that, in the course of yeast evolution, a promoter switches its class with the probability at least ~0.1 per time required for the accumulation of one nucleotide substitution at a non-coding site. Thus, key sequences involved in initiation of transcription evolve with substantial rates in yeast

Mitochondrial pathogenic mutations are population-specific

<p>Abstract</p> <p>Background</p> <p>Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.</p> <p>Results</p> <p>We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.</p> <p>Conclusions</p> <p>Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.</p> <p>Reviewers</p> <p>This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).</p

Rate and breadth of protein evolution are only weakly correlated

<p>Abstract</p> <p>Background</p> <p>Evolution at a protein site can be characterized from two different perspectives, by its rate and by the breadth of the set of acceptable amino acids.</p> <p>Results</p> <p>There is a weak positive correlation between rates and breadths of evolution, both across individual amino acid sites and across proteins.</p> <p>Conclusions</p> <p>Rate and breadth are two distinct, and only weakly correlated, characteristics of protein evolution. The most likely explanation of their positive correlation is heterogeneity of selective constraint, such that less functionally important sites evolve faster and can accept more amino acids.</p> <p>Reviewers</p> <p>This article was reviewed by Eugene V. Koonin, Arcady R. Mushegyan, and Eugene I. Shakhnovich.</p

Extensive parallelism in protein evolution

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Analytic approach to the evolutionary effects of genetic exchange

We present an approximate analytic study of our previously introduced model of evolution including the effects of genetic exchange. This model is motivated by the process of bacterial transformation. We solve for the velocity, the rate of increase of fitness, as a function of the fixed population size, $N$. We find the velocity increases with $\ln N$, eventually saturated at an $N$ which depends on the strength of the recombination process. The analytical treatment is seen to agree well with direct numerical simulations of our model equations

ПРИНЦИПИ КОНСТРУКЦІЇ З НАВІГАЦІЙНО-ПРИЗЕМЛЕНОЮ СИСТЕМОЮ ДЛЯ ЛІТАКІВ МІСЦЕВИХ АВІАЛІНІЙ

The variants of construction and use of surface and side radio equipment are considered in the article, the indexes of quality of the system are certain, priorities are placed for its different modifications.В статье рассмотрены варианты построения и использования систем  наземного и бортового радиооборудования, расставлены приоритеты для различных ее модификаций.У статті розглянуті варіанти побудови і використання наземного і бортового радіоустаткування системи, розставлені пріоритети для різних її модифікацій

Recombination dramatically speeds up evolution of finite populations

We study the role of recombination, as practiced by genetically-competent bacteria, in speeding up Darwinian evolution. This is done by adding a new process to a previously-studied Markov model of evolution on a smooth fitness landscape; this new process allows alleles to be exchanged with those in the surrounding medium. Our results, both numerical and analytic, indicate that for a wide range of intermediate population sizes, recombination dramatically speeds up the evolutionary advance

Improved Design of a Worm Type Instrument for Final Machining of Evolvent Gear Teeth

© 2017 The Authors. Published by Elsevier Ltd. In connection with the absence of possibility to process gear-wheels with large allowance at machining of disk shavers (for example, after the preliminary rolling-up of points), N.V. Smorkalov et al. have worked out the construction of a worm type instrument with a continuous spiral cutting edge. The limitations of this construction were unfavorable terms of cutting wedge work for lack of the structurally executed rake which resulted in the subzero treatment productivity. For simplification of the procedure, regrinding of this instrument and minimization of the nascent "organic" error at regrinding on the outward cylindrical surface, a decision was made to bring in the instrument construction developed by N.V. Smorkalov et al. of positive rake γ, form a radius ditch and two antihunt ribbons breadthways l executed on an outward cylindrical surface. Thus, threading-in of the instrument gets better in metal with shaving deformation diminishing and its tails get better, while the force and cutting power are deminished