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

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

Exact Asymptotic Results for a Model of Sequence Alignment

Finding analytically the statistics of the longest common subsequence (LCS) of a pair of random sequences drawn from c alphabets is a challenging problem in computational evolutionary biology. We present exact asymptotic results for the distribution of the LCS in a simpler, yet nontrivial, variant of the original model called the Bernoulli matching (BM) model which reduces to the original model in the large c limit. We show that in the BM model, for all c, the distribution of the asymptotic length of the LCS, suitably scaled, is identical to the Tracy-Widom distribution of the largest eigenvalue of a random matrix whose entries are drawn from a Gaussian unitary ensemble. In particular, in the large c limit, this provides an exact expression for the asymptotic length distribution in the original LCS problem.Comment: 4 pages Revtex, 2 .eps figures include

Bethe Ansatz in the Bernoulli Matching Model of Random Sequence Alignment

For the Bernoulli Matching model of sequence alignment problem we apply the Bethe ansatz technique via an exact mapping to the 5--vertex model on a square lattice. Considering the terrace--like representation of the sequence alignment problem, we reproduce by the Bethe ansatz the results for the averaged length of the Longest Common Subsequence in Bernoulli approximation. In addition, we compute the average number of nucleation centers of the terraces.Comment: 14 pages, 5 figures (some points are clarified

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

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.

A eubacterial origin for the human tRNA nucleotidyltransferase?

tRNA CCA-termini are generated and maintained by tRNA nucleotidyltransferases. Together with poly(A) polymerases and other enzymes they belong to the nucleotidyltransferase superfamily. However, sequence alignments within this family do not allow to distinguish between CCA-adding enzymes and poly(A) polymerases. Furthermore, due to the lack of sequence information about animal CCA-adding enzymes, identification of corresponding animal genes was not possible so far. Therefore, we looked for the human homolog using the baker's yeast tRNA nucleotidyltransferase as a query sequence in a BLAST search. This revealed that the human gene transcript CGI-47, (\#AF151805) deposited in GenBank is likely to encode such an enzyme. To identify the nature of this protein, the cDNA of the transcript was cloned and the recombinant protein biochemically characterized, indicating that CGI-47 encodes a bona fide CCA-adding enzyme and not a poly(A) polymerase. This confirmed animal CCA-adding enzyme allowed us to identify putative homologs from other animals. Calculation of a neighbor-joining tree, using an alignment of several CCA-adding enzymes, revealed that the animal enzymes resemble more eubacterial ones than eukaryotic plant and fungal tRNA nucleotidyltransferases, suggesting that the animal nuclear cca genes might have been derived from the endosymbiotic progenitor of mitochondria and are therefore of eubacterial origin

Failure of Gauge Invariance in the Nonperturbative Formulation of Massless Lorentz-Violating QED

We consider a Lorentz-violating modification to the fermionic Lagrangian of QED that is known to produce a finite Chern-Simons term at leading order. We compute the second order correction to the one-loop photon self-energy in the massless case using an exact propagator and a nonperturbative formulation of the theory. This nonperturbative theory assigns a definite value to the coefficient of the induced Chern-Simons term; however, we find that the theory fails to preserve gauge invariance at higher orders. We conclude that the specific nonperturbative value of the Chern-Simons coefficient has no special significance.Comment: 8 pages, very minor change

Stationary solutions for the parity-even sector of the CPT-even and Lorentz-covariance-violating term of the standard model extension

In this work, we focus on some properties of the parity-even sector of the CPT-even electrodynamics of the standard model extension. We analyze how the six non-birefringent terms belonging to this sector modify the static and stationary classical solutions of the usual Maxwell theory. We observe that the parity-even terms do not couple the electric and magnetic sectors (at least in the stationary regime). The Green's method is used to obtain solutions for the field strengths E and B at first order in the Lorentz- covariance-violating parameters. Explicit solutions are attained for point-like and spatially extended sources, for which a dipolar expansion is achieved. Finally, it is presented an Earth-based experiment that can lead (in principle) to an upper bound on the anisotropic coefficients as stringent as $(\widetilde{\kappa}_{e-}) ^{ij}<2.9\times10^{-20}.$Comment: 8 pages, revtex style, revised published version, to appear in EPJC (2009