209 research outputs found
The intermediate evolution phase in case of truncated selection
Using methods of statistical physics, we present rigorous theoretical
calculations of Eigen's quasispecies theory with the truncated fitness
landscape which dramatically limits the available sequence space of a
reproducing quasispecies. Depending on the mutation rates, we observe three
phases, a selective one, an intermediate one with some residual order and a
completely randomized phase. Our results are applicable for the general case of
fitness landscape.Comment: 8 page
Quantifying Hopping and Jumping in Facilitated Diffusion of DNA-Binding Proteins
International audienc
Coupling of diagenetic alterations and mechanical properties of Lower Permian siliciclastic sandstones: a pilot study
Initial detrital composition and authigenic alterations during diagenesis of three sandstone types are related to their mechanical properties. Sandstones were prepared for geotechnical standard tests [density, uniaxial compressive strength (UCS), Youngâs modulus (E), strain at failure (Δ)] and thin sections for petrographic analyses (point counting). UCS ranges from 3 to 62 MPa and positively correlates with density (1.75â2.35 g/cm3) and E (0.3â12.7 GPa). Optical porosity is controlling these mechanical parameters and was linked to diagenetic alterations. Diagenetic alterations affecting porosity reduction are the abundance of clay minerals, and the intensity of mechanical and chemical compaction. The latter is controlled by clay mineral coatings on contacts between detrital grains, and the occurrence of authigenic quartz and dolomite. Horizontal contact lengths of grains normalized to their respective particle diameter (effective contact ratio, ECR) and porosity are identified as a control on the mechanical properties UCS and E, reflected by the rock strength index SR. The results of this pilot study suggest that SR is able to predict UCS and E based on petrographic information obtained from the studied samples. These results enhance the understanding of the coupling between mineralogy and geomechanics and highlight the impact of diagenesis on geomechanical behavior
Molecular Evolution in Time Dependent Environments
The quasispecies theory is studied for dynamic replication landscapes. A
meaningful asymptotic quasispecies is defined for periodic time dependencies.
The quasispecies' composition is constantly changing over the oscillation
period. The error threshold moves towards the position of the time averaged
landscape for high oscillation frequencies and follows the landscape closely
for low oscillation frequencies.Comment: 5 pages, 3 figures, Latex, uses Springer documentclass llncs.cl
First modulation of high-frequency polar mesospheric summer echoes by radio heating of the ionosphere
The first high-frequency (HF, 8 MHz) observations of the modulation of polar mesospheric summer echoes (PMSE) by artificial radio heating of the ionosphere are presented and compared to observations at 224 MHz and model predictions. The experiments were performed at the European Incoherent Scatter facility in northern Norway. It is shown that model results are in qualitative and partial quantitative agreement with the observations, supporting the prediction that with certain ranges of ice particle radii and concentration, PMSE at HF radar wavelengths can be enhanced by heating due to the dominance of dust charging over plasma diffusion
Machine Learning in Automated Text Categorization
The automated categorization (or classification) of texts into predefined
categories has witnessed a booming interest in the last ten years, due to the
increased availability of documents in digital form and the ensuing need to
organize them. In the research community the dominant approach to this problem
is based on machine learning techniques: a general inductive process
automatically builds a classifier by learning, from a set of preclassified
documents, the characteristics of the categories. The advantages of this
approach over the knowledge engineering approach (consisting in the manual
definition of a classifier by domain experts) are a very good effectiveness,
considerable savings in terms of expert manpower, and straightforward
portability to different domains. This survey discusses the main approaches to
text categorization that fall within the machine learning paradigm. We will
discuss in detail issues pertaining to three different problems, namely
document representation, classifier construction, and classifier evaluation.Comment: Accepted for publication on ACM Computing Survey
The relationship between the error catastrophe, survival of the flattest, and natural selection
<p>Abstract</p> <p>Background</p> <p>The quasispecies model is a general model of evolution that is generally applicable to replication up to high mutation rates. It predicts that at a sufficiently high mutation rate, quasispecies with higher mutational robustness can displace quasispecies with higher replicative capacity, a phenomenon called "survival of the flattest". In some fitness landscapes it also predicts the existence of a maximum mutation rate, called the error threshold, beyond which the quasispecies enters into error catastrophe, losing its genetic information. The aim of this paper is to study the relationship between survival of the flattest and the transition to error catastrophe, as well as the connection between these concepts and natural selection.</p> <p>Results</p> <p>By means of a very simplified model, we show that the transition to an error catastrophe corresponds to a value of zero for the selective coefficient of the mutant phenotype with respect to the master phenotype, indicating that transition to the error catastrophe is in this case similar to the selection of a more robust species. This correspondence has been confirmed by considering a single-peak landscape in which sequences are grouped with respect to their Hamming distant from the master sequence. When the robustness of a classe is changed by modification of its quality factor, the distribution of the population changes in accordance with the new value of the robustness, although an error catastrophe can be detected at the same values as in the general case. When two quasispecies of different robustness competes with one another, the entry of one of them into error catastrophe causes displacement of the other, because of the greater robustness of the former. Previous works are explicitly reinterpreted in the light of the results obtained in this paper.</p> <p>Conclusions</p> <p>The main conclusion of this paper is that the entry into error catastrophe is a specific case of survival of the flattest acting on phenotypes that differ in the trade-off between replicative ability and mutational robustness. In fact, entry into error catastrophe occurs when the mutant phenotype acquires a selective advantage over the master phenotype. As both entry into error catastrophe and survival of the flattest are caused by natural selection when mutation rate is increased, we propose differentiating between them by the level of selection at which natural selection acts. So we propose to consider the transition to error catastrophe as a phenomenon of intra-quasispecies selection, and survival of the flattest as a phenomenon of inter-quasispecies selection.</p
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