Lorentz Violation and Synchrotron Radiation

We consider the radiation emitted by an ultrarelativistic charged particle moving in a magnetic field, in the presence of an additional Lorentz-violating interaction. In contrast with prior work, we treat a form of Lorentz violation that is represented by a renormalizable operator. Neglecting the radiative reaction force, the particle's trajectory can be determined exactly. The resulting orbit is generally noncircular and does not lie in the place perpendicular to the magnetic field. We do not consider any Lorentz violation in the electromagnetic sector, so the radiation from the accelerated charge can be determined by standard means, and the radiation spectrum will exhibit a Lorentz-violating directional dependence. Using data on emission from the Crab nebula, we can set a bound on a particular combination of Lorentz-violating coefficients at the $6\times10^{-20}$ level.Comment: 14 page

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

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

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

Velocity in Lorentz-Violating Fermion Theories

We consider the role of the velocity in Lorentz-violating fermionic quantum theory, especially emphasizing the nonrelativistic regime. Information about the velocity will be important for the kinematical analysis of scattering and other problems. Working within the minimal standard model extension, we derive new expressions for the velocity. We find that generic momentum and spin eigenstates may not have well-defined velocities. We also demonstrate how several different techniques may be used to shed light on different aspects of the problem. A relativistic operator analysis allows us to study the behavior of the Lorentz-violating Zitterbewegung. Alternatively, by studying the time evolution of Gaussian wave packets, we find that there are Lorentz-violating modifications to the wave packet spreading and the spin structure of the wave function.Comment: 24 page

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

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

Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies

Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions about sequence evolution. Information theory provides an alternative, in the form of mutual information (MI) which is, in principle, an objective and model independent similarity measure. MI can be estimated by concatenating and zipping sequences, yielding thereby the "normalized compression distance". So far this has produced promising results, but with uncontrolled errors. We describe a simple approach to get robust estimates of MI from global pairwise alignments. Using standard alignment algorithms, this gives for animal mitochondrial DNA estimates that are strikingly close to estimates obtained from the alignment free methods mentioned above. Our main result uses algorithmic (Kolmogorov) information theory, but we show that similar results can also be obtained from Shannon theory. Due to the fact that it is not additive, normalized compression distance is not an optimal metric for phylogenetics, but we propose a simple modification that overcomes the issue of additivity. We test several versions of our MI based distance measures on a large number of randomly chosen quartets and demonstrate that they all perform better than traditional measures like the Kimura or log-det (resp. paralinear) distances. Even a simplified version based on single letter Shannon entropies, which can be easily incorporated in existing software packages, gave superior results throughout the entire animal kingdom. But we see the main virtue of our approach in a more general way. For example, it can also help to judge the relative merits of different alignment algorithms, by estimating the significance of specific alignments.Comment: 19 pages + 16 pages of supplementary materia

Simplified amino acid alphabets based on deviation of conditional probability from random background

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.Comment: 9 pages,3figure

T and CPT Symmetries in Entangled Neutral Meson Systems

Genuine tests of an asymmetry under T and/or CPT transformations imply the interchange between in-states and out-states. I explain a methodology to perform model-indepedent separate measurements of the three CP, T and CPT symmetry violations for transitions involving the decay of the neutral meson systems in B- and {\Phi}-factories. It makes use of the quantum-mechanical entanglement only, for which the individual state of each neutral meson is not defined before the decay of its orthogonal partner. The final proof of the independence of the three asymmetries is that no other theoretical ingredient is involved and that the event sample corresponding to each case is different from the other two. The experimental analysis for the measurements of these three asymmetries as function of the time interval {\Delta}t > 0 between the first and second decays is discussed, as well as the significance of the expected results. In particular, one may advance a first observation of true, direct, evidence of Time-Reserval-Violation in B-factories by many standard deviations from zero, without any reference to, and independent of, CP-Violation. In some quantum gravity framework the CPT-transformation is ill-defined, so there is a resulting loss of particle-antiparticle identity. This mechanism induces a breaking of the EPR correlation in the entanglement imposed by Bose statistics to the neutral meson system, the so-called {\omega}-effect. I present results and prospects for the {\omega}-parameter in the correlated neutral meson-antimeson states.Comment: Proc. DISCRETE 2010, Symposium on Prospects in the Physics of Discrete Symmetries, December 2010, Rom