11,264 research outputs found
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
-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
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
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
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
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