Synchrotron and Inverse Compton Constraints on Lorentz Violations for Electrons

We present a method for constraining Lorentz violation in the electron sector, based on observations of the photons emitted by high-energy astrophysical sources. The most important Lorentz-violating operators at the relevant energies are parameterized by a tensor c^{nu mu) with nine independent components. If c is nonvanishing, then there may be either a maximum electron velocity less than the speed of light or a maximum energy for subluminal electrons; both these quantities will generally depend on the direction of an electron's motion. From synchrotron radiation, we may infer a lower bound on the maximum velocity, and from inverse Compton emission, a lower bound on the maximum subluminal energy. With observational data for both these types of emission from multiple celestial sources, we may then place bounds on all nine of the coefficients that make up c. The most stringent bound, on a certain combination of the coefficients, is at the 6 x 10^(-20) level, and bounds on the coefficients individually range from the 7 x 10^(-15) level to the 2 x 10^(-17) level. For most of the coefficients, these are the most precise bounds available, and with newly available data, we can already improve over previous bounds obtained by the same methods.Comment: 28 page

Parallel approach to sliding window sums

Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the advanced vector extension (AVX) instructions available on modern processors, or the parallel compute units on GPUs and FPGAs, would provide a significant performance boost for the bioinformatics applications. We develop a generic vectorized sliding sum algorithm with speedup for window size w and number of processors P is O(P/w) for a generic sliding sum. For a sum with commutative operator the speedup is improved to O(P/log(w)). When applied to the genomic application of minimizer based k-mer table generation using AVX instructions, we obtain a speedup of over 5X.Comment: 10 pages, 5 figure

Genetic Correlations in Mutation Processes

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a critical rate, the underlying tree morphology is almost irrelevant, while mutation rates higher than this critical rate lead to strong tree-dependent correlations. We show analytically that identical critical behavior underlies all multiple point correlations. This behavior generally characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig

A eubacterial origin for the human tRNA nucleotidyltransferase?

tRNA CCA-termini are generated and maintained by tRNA nucleotidyltransferases. Together with poly(A) polymerases and other enzymes they belong to the nucleotidyltransferase superfamily. However, sequence alignments within this family do not allow to distinguish between CCA-adding enzymes and poly(A) polymerases. Furthermore, due to the lack of sequence information about animal CCA-adding enzymes, identification of corresponding animal genes was not possible so far. Therefore, we looked for the human homolog using the baker's yeast tRNA nucleotidyltransferase as a query sequence in a BLAST search. This revealed that the human gene transcript CGI-47, (\#AF151805) deposited in GenBank is likely to encode such an enzyme. To identify the nature of this protein, the cDNA of the transcript was cloned and the recombinant protein biochemically characterized, indicating that CGI-47 encodes a bona fide CCA-adding enzyme and not a poly(A) polymerase. This confirmed animal CCA-adding enzyme allowed us to identify putative homologs from other animals. Calculation of a neighbor-joining tree, using an alignment of several CCA-adding enzymes, revealed that the animal enzymes resemble more eubacterial ones than eukaryotic plant and fungal tRNA nucleotidyltransferases, suggesting that the animal nuclear cca genes might have been derived from the endosymbiotic progenitor of mitochondria and are therefore of eubacterial origin

Exact Asymptotic Results for a Model of Sequence Alignment

Finding analytically the statistics of the longest common subsequence (LCS) of a pair of random sequences drawn from c alphabets is a challenging problem in computational evolutionary biology. We present exact asymptotic results for the distribution of the LCS in a simpler, yet nontrivial, variant of the original model called the Bernoulli matching (BM) model which reduces to the original model in the large c limit. We show that in the BM model, for all c, the distribution of the asymptotic length of the LCS, suitably scaled, is identical to the Tracy-Widom distribution of the largest eigenvalue of a random matrix whose entries are drawn from a Gaussian unitary ensemble. In particular, in the large c limit, this provides an exact expression for the asymptotic length distribution in the original LCS problem.Comment: 4 pages Revtex, 2 .eps figures include

Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Similarity-Detection and Localization

The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a threshold value. The onset of detection is a continuous phase transition which can be viewed as a localization-delocalization transition. The ``fidelity'' of the alignment is the order parameter of that transition; it leads to criteria for the selection of optimal alignment parameters.Comment: 4 pages including 4 figures (308kb post-script file

Consistency analysis of a nonbirefringent Lorentz-violating planar model

In this work analyze the physical consistency of a nonbirefringent Lorentz-violating planar model via the analysis of the pole structure of its Feynman propagators. The nonbirefringent planar model, obtained from the dimensional reduction of the CPT-even gauge sector of the standard model extension, is composed of a gauge and a scalar fields, being affected by Lorentz-violating (LIV) coefficients encoded in the symmetric tensor $\kappa_{\mu\nu}$. The propagator of the gauge field is explicitly evaluated and expressed in terms of linear independent symmetric tensors, presenting only one physical mode. The same holds for the scalar propagator. A consistency analysis is performed based on the poles of the propagators. The isotropic parity-even sector is stable, causal and unitary mode for $0\leq\kappa_{00}<1$. On the other hand, the anisotropic sector is stable and unitary but in general noncausal. Finally, it is shown that this planar model interacting with a $\lambda|\varphi|^{4}-$Higgs field supports compactlike vortex configurations.Comment: 11 pages, revtex style, final revised versio

On the influence of a Coulomb-like potential induced by the Lorentz symmetry breaking effects on the Harmonic Oscillator

In this work, we obtain bound states for a nonrelativistic spin-half neutral particle under the influence of a Coulomb-like potential induced by the Lorentz symmetry breaking effects. We present a new possible scenario of studying the Lorentz symmetry breaking effects on a nonrelativistic quantum system defined by a fixed space-like vector field parallel to the radial direction interacting with a uniform magnetic field along the z-axis. Furthermore, we also discuss the influence of a Coulomb-like potential induced by Lorentz symmetry violation effects on the two-dimensional harmonic oscillator.Comment: 14 pages, no figure, this work has been accepted for publication in The European Physical Journal Plu

Stationary solutions for the parity-even sector of the CPT-even and Lorentz-covariance-violating term of the standard model extension

In this work, we focus on some properties of the parity-even sector of the CPT-even electrodynamics of the standard model extension. We analyze how the six non-birefringent terms belonging to this sector modify the static and stationary classical solutions of the usual Maxwell theory. We observe that the parity-even terms do not couple the electric and magnetic sectors (at least in the stationary regime). The Green's method is used to obtain solutions for the field strengths E and B at first order in the Lorentz- covariance-violating parameters. Explicit solutions are attained for point-like and spatially extended sources, for which a dipolar expansion is achieved. Finally, it is presented an Earth-based experiment that can lead (in principle) to an upper bound on the anisotropic coefficients as stringent as $(\widetilde{\kappa}_{e-}) ^{ij}<2.9\times10^{-20}.$Comment: 8 pages, revtex style, revised published version, to appear in EPJC (2009