Limits on Neutron Lorentz Violation from the Stability of Primary Cosmic Ray Protons

Recent evidence appears to confirm that the ultra-high-energy primary cosmic ray spectrum consists mostly of protons. The fact that these protons can traverse large distances to reach Earth allows us to place bounds on Lorentz violations. The protons neither emit vacuum Cerenkov radiation nor $\beta$-decay into neutrons, and this constrains six previously unmeasured coefficients in the neutron sector at the 5 x 10^(-14) level. Among the coefficients bounded here for the first time are those that control spin-independent boost anisotropy for neutrons. This is a phenomenon which could have existed (in light of the preexisting bounds) without additional fine tuning. There are also similar bounds for others species of hadrons. The bounds on Lorentz violation for neutral pions are particularly strong, at the 4 x 10^(-21) level, eleven orders of magnitude better than previous constraints.Comment: 13 pages, version to appear in Phys. Rev.

Hadronic Lorentz Violation in Chiral Perturbation Theory Including the Coupling to External Fields

If any violation of Lorentz symmetry exists in the hadron sector, its ultimate origins must lie at the quark level. We continue the analysis of how the theories at these two levels are connected, using chiral perturbation theory. Considering a two-flavor quark theory, with dimension-4 operators that break Lorentz symmetry, we derive a low-energy theory of pions and nucleons that is invariant under local chiral transformations and includes the coupling to external fields. The pure meson and baryon sectors, as well as the couplings between them and the couplings to external electromagnetic and weak gauge fields, contain forms of Lorentz violation which depend on linear combinations of quark-level coefficients. In particular, at leading order the electromagnetic couplings depend on the very same combinations as appear in the free particle propagators. This means that observations of electromagnetic processes involving hadrons--such as vacuum Cerenkov radiation, which may be allowed in Lorentz-violating theories--can only reliably constrain certain particular combinations of quark coefficients.Comment: 21 page

Statistical Time Series Models of Pilot Control with Applications to Instrument Discrimination

A general description of the methodology used in obtaining the transfer function models and verification of model fidelity, frequency domain plots of the modeled transfer functions, numerical results obtained from an analysis of poles and zeroes obtained from z plane to s-plane conversions of the transfer functions, and the results of a study on the sequential introduction of other variables, both exogenous and endogenous into the loop are contained

Photon Decay at the Schwarzschild Horizon

A recent proposal that gravity theory is an emergent phenomenon also entails the possibility of photon decay near the Schwarzschild event horizon. We present a possible mechanism for such decay, which utilizes a dimensional reduction near the horizon.Comment: 11 pages, no figure

Laboratory Bounds on Electron Lorentz Violation

Violations of Lorentz boost symmetry in the electron and photon sectors can be constrained by studying several different high-energy phenomenon. Although they may not lead to the strongest bounds numerically, measurements made in terrestrial laboratories produce the most reliable results. Laboratory bounds can be based on observations of synchrotron radiation, as well as the observed absences of vacuum Cerenkov radiation. Using measurements of synchrotron energy losses at LEP and the survival of TeV photons, we place new bounds on the three electron Lorentz violation coefficients c_(TJ), at the 3 x 10^(-13) to 6 x 10^(-15) levels.Comment: 18 page

Distributed BLAST in a grid computing context

The Basic Local Alignment Search Tool (BLAST) is one of the best known sequence comparison programs available in bioinformatics. It is used to compare query sequences to a set of target sequences, with the intention of finding similar sequences in the target set. Here, we present a distributed BLAST service which operates over a set of heterogeneous Grid resources and is made available through a Globus toolkit v.3 Grid service. This work has been carried out in the context of the BRIDGES project, a UK e-Science project aimed at providing a Grid based environment for biomedical research. Input consisting of multiple query sequences is partitioned into sub-jobs on the basis of the number of idle compute nodes available and then processed on these in batches. To achieve this, we have implemented our own Java-based scheduler which distributes sub-jobs across an array of resources utilizing a variety of local job scheduling systems

Pairwise alignment incorporating dipeptide covariation

Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for pairwise sequence alignment, but it ignores information that could conceivably increase the power of remote homolog detection. We examine the validity of this assumption by constructing extended substitution matrixes that encapsulate the observed correlations between neighboring sites, by developing an efficient and rigorous algorithm for pairwise protein sequence alignment that incorporates these local substitution correlations, and by assessing the ability of this algorithm to detect remote homologies. Results: Our analysis indicates that local correlations between substitutions are not strong on the average. Furthermore, incorporating local substitution correlations into pairwise alignment did not lead to a statistically significant improvement in remote homology detection. Therefore, the standard assumption that individual residues within protein sequences evolve independently of neighboring positions appears to be an efficient and appropriate approximation

Statistical Mechanics and Lorentz Violation

The theory of statistical mechanics is studied in the presence of Lorentz-violating background fields. The analysis is performed using the Standard-Model Extension (SME) together with a Jaynesian formulation of statistical inference. Conventional laws of thermodynamics are obtained in the presence of a perturbed hamiltonian that contains the Lorentz violating terms. As an example, properties of the nonrelativistic ideal gas are calculated in detail. To lowest order in Lorentz violation, the scalar thermodynamic variables are only corrected by a rotationally invariant combination of parameters that mimics a (frame dependent) effective mass. Spin couplings can induce a temperature independent polarization in the classical gas that is not present in the conventional case. Precision measurements in the residual expectation values of the magnetic moment of Fermi gases in the limit of high temperature may provide interesting limits on these parameters.Comment: 7 pages, revte

Back-translation for discovering distant protein homologies

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. To cope with this situation, we propose a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. This allows us to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.Comment: The 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009

HMMER web server: interactive sequence similarity searching

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them