13,795 research outputs found
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
Gauge Invariance and the Pauli-Villars Regulator in Lorentz- and CPT-Violating Electrodynamics
We examine the nonperturbative structure of the radiatively induced
Chern-Simons term in a Lorentz- and CPT-violating modification of QED. Although
the coefficient of the induced Chern-Simons term is in general undetermined,
the nonperturbative theory appears to generate a definite value. However, the
CPT-even radiative corrections in this same formulation of the theory generally
break gauge invariance. We show that gauge invariance may yet be preserved
through the use of a Pauli-Villars regulator, and, contrary to earlier
expectations, this regulator does not necessarily give rise to a vanishing
Chern-Simons term. Instead, two possible values of the Chern-Simons coefficient
are allowed, one zero and one nonzero. This formulation of the theory therefore
allows the coefficient to vanish naturally, in agreement with experimental
observations.Comment: 8 page
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
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
Asymptotically Universal Crossover in Perturbation Theory with a Field Cutoff
We discuss the crossover between the small and large field cutoff (denoted
x_{max}) limits of the perturbative coefficients for a simple integral and the
anharmonic oscillator. We show that in the limit where the order k of the
perturbative coefficient a_k(x_{max}) becomes large and for x_{max} in the
crossover region, a_k(x_{max}) is proportional to the integral from -infinity
to x_{max} of e^{-A(x-x_0(k))^2}dx. The constant A and the function x_0(k) are
determined empirically and compared with exact (for the integral) and
approximate (for the anharmonic oscillator) calculations. We discuss how this
approach could be relevant for the question of interpolation between
renormalization group fixed points.Comment: 15 pages, 11 figs., improved and expanded version of hep-th/050304
NCBI BLAST: a better web interface
Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement
Correction, improvement and model verification of CARE 3, version 3
An independent verification of the CARE 3 mathematical model and computer code was conducted and reported in NASA Contractor Report 166096, Review and Verification of CARE 3 Mathematical Model and Code: Interim Report. The study uncovered some implementation errors that were corrected and are reported in this document. The corrected CARE 3 program is called version 4. Thus the document, correction. improvement, and model verification of CARE 3, version 3 was written in April 1984. It is being published now as it has been determined to contain a more accurate representation of CARE 3 than the preceding document of April 1983. This edition supercedes NASA-CR-166122 entitled, 'Correction and Improvement of CARE 3,' version 3, April 1983
Biodiversity informatics: the challenge of linking data and the role of shared identifiers
A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers
An Alternative Model of Amino Acid Replacement
The observed correlations between pairs of homologous protein sequences are
typically explained in terms of a Markovian dynamic of amino acid substitution.
This model assumes that every location on the protein sequence has the same
background distribution of amino acids, an assumption that is incompatible with
the observed heterogeneity of protein amino acid profiles and with the success
of profile multiple sequence alignment. We propose an alternative model of
amino acid replacement during protein evolution based upon the assumption that
the variation of the amino acid background distribution from one residue to the
next is sufficient to explain the observed sequence correlations of homologs.
The resulting dynamical model of independent replacements drawn from
heterogeneous backgrounds is simple and consistent, and provides a unified
homology match score for sequence-sequence, sequence-profile and
profile-profile alignment.Comment: Minor improvements. Added figure and reference
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