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

Quantification of the differences between quenched and annealed averaging for RNA secondary structures

The analytical study of disordered system is usually difficult due to the necessity to perform a quenched average over the disorder. Thus, one may resort to the easier annealed ensemble as an approximation to the quenched system. In the study of RNA secondary structures, we explicitly quantify the deviation of this approximation from the quenched ensemble by looking at the correlations between neighboring bases. This quantified deviation then allows us to propose a constrained annealed ensemble which predicts physical quantities much closer to the results of the quenched ensemble without becoming technically intractable.Comment: 9 pages, 14 figures, submitted to Phys. Rev.

Clustering with shallow trees

We propose a new method for hierarchical clustering based on the optimisation of a cost function over trees of limited depth, and we derive a message--passing method that allows to solve it efficiently. The method and algorithm can be interpreted as a natural interpolation between two well-known approaches, namely single linkage and the recently presented Affinity Propagation. We analyze with this general scheme three biological/medical structured datasets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.Comment: 11 pages, 7 figure

CPT and Lorentz violation as signatures for Planck-scale physics

In recent years, the breakdown of spacetime symmetries has been identified as a promising research field in the context of Planck-scale phenomenology. For example, various theoretical approaches to the quantum-gravity problem are known to accommodate minute violations of CPT invariance. This talk covers various topics within this research area. In particular, some mechanisms for spacetime-symmetry breaking as well as the Standard-Model Extension (SME) test framework will be reviewed; the connection between CPT and Lorentz invariance in quantum field theory will be exposed; and various experimental CPT tests with emphasis on matter--antimatter comparisons will be discussed.Comment: 6 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

Non-local on-shell field redefinition for the SME

This work instigates a study of non-local field mappings within the Lorentz- and CPT-violating Standard-Model Extension (SME). An example of such a mapping is constructed explicitly, and the conditions for the existence of its inverse are investigated. It is demonstrated that the associated field redefinition can remove b-type Lorentz violation from free SME fermions in certain situations. These results are employed to obtain explicit expressions for the corresponding Lorentz-breaking momentum-space eigenspinors and their orthogonality relations.Comment: 12 pages, REVTeX

The Casimir Force in a Lorentz Violating Theory

We study the effects of the minimal extension of the standard model including Lorentz violation on the Casimir force between two parallel conducting plates in vacuum. We provide explicit solutions for the electromagnetic field using scalar field analogy, for both the cases in which the Lorentz violating terms come from the CPT-even or CPT-odd terms. We also calculate the effects of the Lorentz violating terms for a fermion field between two parallel conducting plates and analyze the modifications of the Casimir force due to the modifications of the Dirac equation. In all cases under consideration, the standard formulas for the Casimir force are modified by either multiplicative or additive correction factors, the latter case exhibiting different dependence on the distance between the plates.Comment: 20 pages, no figures, references added, accepted for publication in Phys. Rev.