Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure

Background: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees. Different parameter combinations chosen for the multiple alignment may result in different phylogenies. A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial DNA. Result: In this work, we present an application of the RCM method to reconstruct robust phylogenetic trees using sequence data for genus Galanthus obtained from different regions in Turkey. Phylogenies have been analyzed using nuclear and chloroplast DNA sequences. Results showed that, the tree obtained from nuclear ribosomal RNA gene sequences was more robust, while the tree obtained from the chloroplast DNA showed a higher degree of variation. Conclusions: Phylogenies generated by Relative Complexity Measure were found to be robust and results of RCM were more reliable than the compared techniques. Particularly, to overcome MSA-based problems, RCM seems to be a reasonable way and a good alternative to MSA-based phylogenetic analysis. We believe our method will become a mainstream phylogeny construction method especially for the highly variable sequence families where the accuracy of the MSA heavily depends on the alignment parameters

Conformal Ricci collineations of static spherically symmetric spacetimes

Conformal Ricci collineations of static spherically symmetric spacetimes are studied. The general form of the vector fields generating conformal Ricci collineations is found when the Ricci tensor is non-degenerate, in which case the number of independent conformal Ricci collineations is \emph{fifteen}; the maximum number for 4-dimensional manifolds. In the degenerate case it is found that the static spherically symmetric spacetimes always have an infinite number of conformal Ricci collineations. Some examples are provided which admit non-trivial conformal Ricci collineations, and perfect fluid source of the matter

Probability densities for the sums of iterates of the sine-circle map in the vicinity of the quasi-periodic edge of chaos

We investigate the probability density of rescaled sum of iterates of sine-circle map within quasi-periodic route to chaos. When the dynamical system is strongly mixing (i.e., ergodic), standard Central Limit Theorem (CLT) is expected to be valid, but at the edge of chaos where iterates have strong correlations, the standard CLT is not necessarily to be valid anymore. We discuss here the main characteristics of the central limit behavior of deterministic dynamical systems which exhibit quasi-periodic route to chaos. At the golden-mean onset of chaos for the sine-circle map, we numerically verify that the probability density appears to converge to a q-Gaussian with q<1 as the golden mean value is approached.Comment: 7 pages, 7 figures, 1 tabl

Droplet Spreading Process Impact on Ignition Characteristics of Condensed Materials

Mathematical simulation of condensed material solid-phase ignition in the context of the in-situ heating by the melted or heated to high temperature metal droplet was carried out. The authors developed the mathematical model that describes the heat transfer process in the "droplet – condensed material" system by the system of heat transfer equations with boundary and initial conditions. The problem is solved by the finite difference method. Four modes of condensed material ignition that are distinguished by the temperature range of every mode were identified for standard conditions of the in-situ heat effect

Prediction of peptides binding to MHC class I and II alleles by temporal motif mining

Background: MHC (Major Histocompatibility Complex) is a key player in the immune response of most vertebrates. The computational prediction of whether a given antigenic peptide will bind to a specific MHC allele is important in the development of vaccines for emerging pathogens, the creation of possibilities for controlling immune response, and for the applications of immunotherapy. One of the problems that make this computational prediction difficult is the detection of the binding core region in peptides, coupled with the presence of bulges and loops causing variations in the total sequence length. Most machine learning methods require the sequences to be of the same length to successfully discover the binding motifs, ignoring the length variance in both motif mining and prediction steps. In order to overcome this limitation, we propose the use of time-based motif mining methods that work position-independently. Results: The prediction method was tested on a benchmark set of 28 different alleles for MHC class I and 27 different alleles for MHC class II. The obtained results are comparable to the state of the art methods for both MHC classes, surpassing the published results for some alleles. The average prediction AUC values are 0.897 for class I, and 0.858 for class II. Conclusions: Temporal motif mining using partial periodic patterns can capture information about the sequences well enough to predict the binding of the peptides and is comparable to state of the art methods in the literature. Unlike neural networks or matrix based predictors, our proposed method does not depend on peptide length and can work with both short and long fragments. This advantage allows better use of the available training data and the prediction of peptides of uncommon lengths

Analysis of return distributions in the coherent noise model

The return distributions of the coherent noise model are studied for the system size independent case. It is shown that, in this case, these distributions are in the shape of q-Gaussians, which are the standard distributions obtained in nonextensive statistical mechanics. Moreover, an exact relation connecting the exponent $\tau$ of avalanche size distribution and the q value of appropriate q-Gaussian has been obtained as q=(tau+2)/tau. Making use of this relation one can easily determine the q parameter values of the appropriate q-Gaussians a priori from one of the well-known exponents of the system. Since the coherent noise model has the advantage of producing different tau values by varying a model parameter \sigma, clear numerical evidences on the validity of the proposed relation have been achieved for different cases. Finally, the effect of the system size has also been analysed and an analytical expression has been proposed, which is corroborated by the numerical results.Comment: 14 pages, 3 fig

Two-dimensional maps at the edge of chaos: Numerical results for the Henon map

The mixing properties (or sensitivity to initial conditions) of two-dimensional Henon map have been explored numerically at the edge of chaos. Three independent methods, which have been developed and used so far for the one-dimensional maps, have been used to accomplish this task. These methods are (i)measure of the divergence of initially nearby orbits, (ii)analysis of the multifractal spectrum and (iii)computation of nonextensive entropy increase rates. The obtained results strongly agree with those of the one-dimensional cases and constitute the first verification of this scenario in two-dimensional maps. This obviously makes the idea of weak chaos even more robust.Comment: 4 pages, 3 figure

Nonadditive entropy and nonextensive statistical mechanics - Some central concepts and recent applications

We briefly review central concepts concerning nonextensive statistical mechanics, based on the nonadditive entropy $S_q=k\frac{1-\sum_{i}p_i^q}{q-1} (q \in {\cal R}; S_1=-k\sum_{i}p_i \ln p_i)$. Among others, we focus on possible realizations of the $q$-generalized Central Limit Theorem, including at the edge of chaos of the logistic map, and for quasi-stationary states of many-body long-range-interacting Hamiltonian systems.Comment: 15 pages, 9 figs., to appear in Journal of Physics: Conf.Series (IOP, 2010

Status of the PANDA barrel DIRC

The PANDA experiment at the future Facility for Antiproton and Ion Research in Europe GmbH (FAIR) at GSI, Darmstadt will study fundamental questions of hadron physics and QCD using high-intensity cooled antiproton beams with momenta between 1.5 and 15 GeV/c. Hadronic PID in the barrel region of the PANDA detector will be provided by a DIRC (Detection of Internally Reflected Cherenkov light) counter. The design is based on the successful BABAR DIRC with several key improvements, such as fast photon timing and a compact imaging region. Detailed Monte Carlo simulation studies were performed for DIRC designs based on narrow bars or wide plates with a variety of focusing solutions. The performance of each design was characterized in terms of photon yield and single photon Cherenkov angle resolution and a maximum likelihood approach was used to determine the π/K separation. Selected design options were implemented in prototypes and tested with hadronic particle beams at GSI and CERN. This article describes the status of the design and R&#38;D for the PANDA Barrel DIRC detector, with a focus on the performance of different DIRC designs in simulation and particle beams