Forecasts of solar and geomagnetic activity

Forecasts of solar and geomagnetic activity are critical since these quantities are such important inputs to the thermospheric density models. At this time in the history of solar science there is no way to make such a forecast from first principles. Physical theory applied to the Sun is developing rapidly, but is still primitive. Techniques used for forecasting depend upon the observations over about 130 years, which is only twelve solar cycles. It has been noted that even-numbered cycles systematically tend to be smaller than the odd-numbered ones by about 20 percent. Another observation is that for the last 12 cycle pairs, an even-numbered sunspot cycle looks rather like the next odd-numbered cycle, but with the top cut off. These observations are examples of approximate periodicities that forecasters try to use to achieve some insight into the nature of an upcoming cycle. Another new and useful forecasting aid is a correlation that has been noted between geomagnetic indices and the size of the next solar cycle. Some best estimates are given concerning both activities

On the possible sources of gravitational wave bursts detectable today

We discuss the possibility that galactic gravitational wave sources might give burst signals at a rate of several events per year, detectable by state-of-the-art detectors. We are stimulated by the results of the data collected by the EXPLORER and NAUTILUS bar detectors in the 2001 run, which suggest an excess of coincidences between the two detectors, when the resonant bars are orthogonal to the galactic plane. Signals due to the coalescence of galactic compact binaries fulfill the energy requirements but are problematic for lack of known candidates with the necessary merging rate. We examine the limits imposed by galactic dynamics on the mass loss of the Galaxy due to GW emission, and we use them to put constraints also on the GW radiation from exotic objects, like binaries made of primordial black holes. We discuss the possibility that the events are due to GW bursts coming repeatedly from a single or a few compact sources. We examine different possible realizations of this idea, such as accreting neutron stars, strange quark stars, and the highly magnetized neutron stars (``magnetars'') introduced to explain Soft Gamma Repeaters. Various possibilities are excluded or appear very unlikely, while others at present cannot be excluded.Comment: 24 pages, 20 figure

Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats

<p>Abstract</p> <p>Background</p> <p>Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used to study primary periodicities in DNA sequences. Here we investigate the application of DFT method to identify and study alphoid higher order repeats.</p> <p>Results</p> <p>We used method based on DFT with mapping of symbolic into numerical sequence to identify and study alphoid higher order repeats (HOR). For HORs the power spectrum shows equidistant frequency pattern, with characteristic two-level hierarchical organization as signature of HOR. Our case study was the 16 mer HOR tandem in AC017075.8 from human chromosome 7. Very long array of equidistant peaks at multiple frequencies (more than a thousand higher harmonics) is based on fundamental frequency of 16 mer HOR. Pronounced subset of equidistant peaks is based on multiples of the fundamental HOR frequency (multiplication factor <it>n </it>for <it>n</it>mer) and higher harmonics. In general, <it>n</it>mer HOR-pattern contains equidistant secondary periodicity peaks, having a pronounced subset of equidistant primary periodicity peaks. This hierarchical pattern as signature for HOR detection is robust with respect to monomer insertions and deletions, random sequence insertions etc. For a monomeric alphoid sequence only primary periodicity peaks are present. The 1/<it>f</it>^{<it>β </it>}– noise and periodicity three pattern are missing from power spectra in alphoid regions, in accordance with expectations.</p> <p>Conclusion</p> <p>DFT provides a robust detection method for higher order periodicity. Easily recognizable HOR power spectrum is characterized by hierarchical two-level equidistant pattern: higher harmonics of the fundamental HOR-frequency (secondary periodicity) and a subset of pronounced peaks corresponding to constituent monomers (primary periodicity). The number of lower frequency peaks (secondary periodicity) below the frequency of the first primary periodicity peak reveals the size of <it>n</it>mer HOR, i.e., the number <it>n </it>of monomers contained in consensus HOR.</p

Anomalous relaxation of density waves in a ring-exchange system

We present the analysis of the slowing down exhibited by stochastic dynamics of a ring-exchange model on a square lattice, by means of numerical simulations. We find the preservation of coarse-grained memory of initial state of density-wave types for unexpectedly long times. This behavior is inconsistent with the prediction from a low frequency continuum theory developed by assuming a mean field solution. Through a detailed analysis of correlation functions of the dynamically active regions, we exhibit an unconventional transient long ranged structure formation in a direction which is featureless for the initial condition, and argue that its slow melting plays a crucial role in the slowing-down mechanism. We expect our results to be relevant also for the dynamics of quantum ring-exchange dynamics of hard-core bosons.Comment: 14 pages, 13 figure

Approximate Circular Pattern Matching

We investigate the complexity of approximate circular pattern matching (CPM, in short) under the Hamming and edit distance. Under each of these two basic metrics, we are given a length-n text T, a length-m pattern P, and a positive integer threshold k, and we are to report all starting positions (called occurrences) of fragments of T that are at distance at most k from some cyclic rotation of P. In the decision version of the problem, we are to check if there is any such occurrence. All previous results for approximate CPM were either average-case upper bounds or heuristics, with the exception of the work of Charalampopoulos et al. [CKP+, JCSS'21], who considered only the Hamming distance. For the reporting version of the approximate CPM problem, under the Hamming distance we improve upon the main algorithm of [CKP+, JCSS'21] from O(n+(n/m) k4) to O(n+(n/m) k3 log log k) time; for the edit distance, we give an O(nk2)-time algorithm. Notably, for the decision versions and wide parameter-ranges, we give algorithms whose complexities are almost identical to the state-of-the-art for standard (i.e., non-circular) approximate pattern matching: For the decision version of the approximate CPM problem under the Hamming distance, we obtain an O(n + (n/m) k2 log k/ log log k)-time algorithm, which works in O(n) time whenever k = O( p mlog log m/logm). In comparison, the fastest algorithm for the standard counterpart of the problem, by Chan et al. [CGKKP, STOC'20], runs in O(n) time only for k = O(√ m). We achieve this result via a reduction to a geometric problem by building on ideas from [CKP+, JCSS'21] and Charalampopoulos et al. [CKW, FOCS'20]. For the decision version of the approximate CPM problem under the edit distance, the O(nk log3 k) runtime of our algorithm near matches the O(nk) runtime of the Landau-Vishkin algorithm [LV, J. Algorithms'89] for approximate pattern matching under edit distance; the latter algorithm remains the fastest known for k = Ω(m2/5). As a stepping stone, we propose an O(nk log3 k)-time algorithm for solving the Longest Prefix k-Approximate Match problem, proposed by Landau et al. [LMS, SICOMP'98], for all k ∈ {1, , k}. Our algorithm is based on Tiskin's theory of seaweeds [Tiskin, Math. Comput. Sci.'08], with recent advancements (see Charalampopoulos et al. [CKW, FOCS'22]), and on exploiting the seaweeds' relation to Monge matrices. In contrast, we obtain a conditional lower bound that suggests a polynomial separation between approximate CPM under the Hamming distance over the binary alphabet and its non-circular counterpart. We also show that a strongly subquadratic-time algorithm for the decision version of approximate CPM under edit distance would refute the Strong Exponential Time Hypothesis

Approximate Covers of Strings

Tato práce staví na publikaci Kędzierského and Radoszewského, kteří představili vylepšené polynomiální algoritmy řešící problém k-přibližných pokrytí řetězců nad Hammingovou, Levenshteinovou a váženou editační vzdáleností. Práce tyto algoritmy důkladně popisuje, vysvětluje a poskytuje jiný úhel pohledu. Algoritmy jsou implementovány a problémy, které řesí jsou zasazeny do kontextu dalších pravidelností v řetězcích. Implementce je experimentálně otestována a jsou popsány hlavní implementační kroky.This thesis builds upon recent findings of Kędzierski and Radoszewski who presented improved polynomial time algorithms for computing k-approximate covers of strings under Hamming, Levenshtein and weighted edit distance. These algorithms are thoroughly described providing explanations from different point of view. The algorithms are implemented and the problems they solve are inset into the context of other string regularities. The implementation is experimentally evaluated alongside with the description of the main implementation decisions

Observation of Majorana Fermions in Ferromagnetic Atomic Chains on a Superconductor

Majorana fermions are predicted to localize at the edge of a topological superconductor, a state of matter that can form when a ferromagnetic system is placed in proximity to a conventional superconductor with strong spin-orbit interaction. With the goal of realizing a one-dimensional topological superconductor, we have fabricated ferromagnetic iron (Fe) atomic chains on the surface of superconducting lead (Pb). Using high-resolution spectroscopic imaging techniques, we show that the onset of superconductivity, which gaps the electronic density of states in the bulk of the Fe chains, is accompanied by the appearance of zero energy end states. This spatially resolved signature provides strong evidence, corroborated by other observations, for the formation of a topological phase and edge-bound Majorana fermions in our atomic chains.Comment: 18 pages, 5 figures, and supplementary information. appears in Science (2014

Statistical methods for detecting periodic fragments in DNA sequence data

<p>Abstract</p> <p>Background</p> <p>Period 10 dinucleotides are structurally and functionally validated factors that influence the ability of DNA to form nucleosomes, histone core octamers. Robust identification of periodic signals in DNA sequences is therefore required to understand nucleosome organisation in genomes. While various techniques for identifying periodic components in genomic sequences have been proposed or adopted, the requirements for such techniques have not been considered in detail and confirmatory testing for a priori specified periods has not been developed.</p> <p>Results</p> <p>We compared the estimation accuracy and suitability for confirmatory testing of autocorrelation, discrete Fourier transform (DFT), integer period discrete Fourier transform (IPDFT) and a previously proposed Hybrid measure. A number of different statistical significance procedures were evaluated but a blockwise bootstrap proved superior. When applied to synthetic data whose period-10 signal had been eroded, or for which the signal was approximately period-10, the Hybrid technique exhibited superior properties during exploratory period estimation. In contrast, confirmatory testing using the blockwise bootstrap procedure identified IPDFT as having the greatest statistical power. These properties were validated on yeast sequences defined from a ChIP-chip study where the Hybrid metric confirmed the expected dominance of period-10 in nucleosome associated DNA but IPDFT identified more significant occurrences of period-10. Application to the whole genomes of yeast and mouse identified ~ 21% and ~ 19% respectively of these genomes as spanned by period-10 nucleosome positioning sequences (NPS).</p> <p>Conclusions</p> <p>For estimating the dominant period, we find the Hybrid period estimation method empirically to be the most effective for both eroded and approximate periodicity. The blockwise bootstrap was found to be effective as a significance measure, performing particularly well in the problem of period detection in the presence of eroded periodicity. The autocorrelation method was identified as poorly suited for use with the blockwise bootstrap. Application of our methods to the genomes of two model organisms revealed a striking proportion of the yeast and mouse genomes are spanned by NPS. Despite their markedly different sizes, roughly equivalent proportions (19-21%) of the genomes lie within period-10 spans of the NPS dinucleotides {<it>AA, TT, TA</it>}. The biological significance of these regions remains to be demonstrated. To facilitate this, the genomic coordinates are available as Additional files 1, 2, and 3 in a format suitable for visualisation as tracks on popular genome browsers.</p> <p>Reviewers</p> <p>This article was reviewed by Prof Tomas Radivoyevitch, Dr Vsevolod Makeev (nominated by Dr Mikhail Gelfand), and Dr Rob D Knight.</p