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

Extensive parallelism in protein evolution

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

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

Protein structural variation in computational models and crystallographic data

Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validation is typically limited to individual modes for a single protein. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational variance. Normal modes from four simple elastic network model potentials and from the CHARMM forcefield are calculated for a data set of 83 diverse, ultrahigh resolution crystal structures. While all five potentials provide good predictions of the magnitude of flexibility, the methods that consider all atoms have a clear edge at prediction of directionality, and the CHARMM potential produces the best agreement. The low-frequency modes from different potentials are similar, but those computed from the CHARMM potential show the greatest difference from the elastic network models. This was illustrated by computing the dynamic correlation matrices from different potentials for a PDZ domain structure. Comparison of normal mode results with anisotropic temperature factors opens the possibility of using ultrahigh resolution crystallographic data as a quantitative measure of molecular flexibility. The comprehensive evaluation demonstrates the costs and benefits of using normal mode potentials of varying complexity. Comparison of the dynamic correlation matrices suggests that a combination of topological and chemical potentials may help identify residues in which chemical forces make large contributions to intramolecular coupling.Comment: 17 pages, 4 figure

Rates of SARS-COV-2 transmission and vaccination impact the fate of vaccine-resistant strains

Se considera que las vacunas son la mejor solución para controlar la actual pandemia por SARS-CoV-2. Sin embargo, la proliferación de cepas resistentes a las vacunas puede ser demasiado rápida para que su aplicación alivie la propagación de la pandemia, así como sus consecuencias económicas y sociales. Para cuantificar y caracterizar el riesgo de este escenario, utilizamos un modelo SIR con una dinámica estocástica para estudiar la probabilidad de aparición y transmisión de cepas resistentes a la vacuna. Usando parámetros que repliquen de manera realista la transmisión del SARS-CoV-2, modelizamos el patrón en forma de olas de la pandemia y consideramos el impacto que el ritmo de vacunación y la intensidad de las medidas de contención adoptadas tienen sobre la probabilidad de aparición de cepas resistentes a la vacuna. Como era de esperar, un ritmo rápido de vacunación disminuye la probabilidad de aparición de una cepa resistente a la vacuna. Sin embargo, aunque en principio pueda parecer contraintuitivo, cuando se produce una relajación de las restricciones en el momento en el que la mayoría de la población ya ha sido vacunada, la probabilidad de aparición de una cepa resistente a la vacuna aumenta considerablemente. En consecuencia, un período de contención estricta de la transmisión cerca del final de la campaña de vacunación puede reducir sustancialmente la probabilidad del establecimiento de cepas resistentes a la vacuna. Estos resultados, por tanto, sugieren la conveniencia de mantener las medidas y los protocolos de prevención durante toda la duración de la campaña de vacunación.Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. These results, therefore, suggest the convenience of maintaining non-pharmaceutical interventions and prevention protocols throughout the entire vaccination period

ПРИНЦИПИ УТВОРЕННЯ ПАРАМЕТРИЧНИХ ВУЗЛІВ КІНЦЕВОГО ПУНКТУ КЕРУЮЧОЇ СИСТЕМИ ТРАНСПОРТНОГО ЗАСОБУ, НЕУКОМПЛЕКТОВАНОГО АНТЕННОЮ ДЛЯ ПОЛЬОТУ

The principles of formation of the vector of distance D from unmanned aerial vehicle UAV to transponderbeacon,and its velocity V­­k, which are necessary for on board calculation of the UAV motion parameters.Показанны принципы формирования векторов дальности D от беспилотного летательного аппарата к маяку- ответчику,его скорость к V­­k, необходимые для вычисления на борту БПЛА параметров его движения.Показані принципи формування векторів дальності D від безпілотного літального апарату до маяка-відповідача ,та його швидкості V­­k , необхідної для обчислення на борту БПЛА параметра його руху

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