BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences

A computer program, BRUCE, was developed for the identification of transfer‐messenger RNA (tmRNA) genes. The program employs heuristic algorithms to search for a tRNAAla‐like secondary structure surrounding a short sequence encoding the tag peptide. In the 57 completely sequenced bacterial genomes where tmRNA genes have been reported previously, BRUCE identified all with no false positives. In addition, BRUCE found 99 of the 100 tmRNAs identified previously in other bacteria, red chloroplasts and cyanelles. The output of the program reports the proposed tRNA secondary structure, the tmRNA gene sequence and the tag peptide

String Effects on Fermi--Dirac Correlation Measurements

We investigate some recent measurements of Fermi--Dirac correlations by the LEP collaborations indicating surprisingly small source radii for the production of baryons in $e^+e^-$-annihilation at the $Z^0$ peak. In the hadronization models there are besides the Fermi--Dirac correlation effect also a strong dynamical (anti-)correlation. We demonstrate that the extraction of the pure FD effect is highly dependent on a realistic Monte Carlo event generator, both for separation of those dynamical correlations which are not related to Fermi--Dirac statistics, and for corrections of the data and background subtractions. Although the model can be tuned to well reproduce single particle distributions, there are large model-uncertainties when it comes to correlations between identical baryons. We therefore, unfortunately, have to conclude that it is at present not possible to make any firm conclusion about the source radii relevant for baryon production at LEP

Event-by-event fluctuations of the charged particle ratio from non-equilibrium transport theory

The event by event fluctuations of the ratio of positively to negatively charged hadrons are predicted within the UrQMD model. Corrections for finite acceptance and finite net charge are derived. These corrections are relevant to compare experimental data and transport model results to previous predictions. The calculated fluctuations at RHIC and SPS energies are shown to be compatible with a hadron gas. Thus, deviating by a factor of 3 from the predictions for a thermalized quark-gluon plasma.Comment: This paper clarifies the previous predictions of Jeon and Koch (hep-ph/0003168) and addresses issues raised in hep-ph/0006023. 2 Figures, 10pp, uses RevTe

Relativistic Two-stream Instability

We study the (local) propagation of plane waves in a relativistic, non-dissipative, two-fluid system, allowing for a relative velocity in the "background" configuration. The main aim is to analyze relativistic two-stream instability. This instability requires a relative flow -- either across an interface or when two or more fluids interpenetrate -- and can be triggered, for example, when one-dimensional plane-waves appear to be left-moving with respect to one fluid, but right-moving with respect to another. The dispersion relation of the two-fluid system is studied for different two-fluid equations of state: (i) the "free" (where there is no direct coupling between the fluid densities), (ii) coupled, and (iii) entrained (where the fluid momenta are linear combinations of the velocities) cases are considered in a frame-independent fashion (eg. no restriction to the rest-frame of either fluid). As a by-product of our analysis we determine the necessary conditions for a two-fluid system to be causal and absolutely stable and establish a new constraint on the entrainment.Comment: 15 pages, 2 eps-figure

The Rumsfeld Effect: The unknown unknown

A set of studies tested whether people can use awareness of ignorance to provide enhanced test consistency over time if they are allowed to place uncertain items into a “don’t know” category. For factual knowledge this did occur, but for a range of other forms of knowledge relating to conceptual knowledge and personal identity, no such effect was seen. Known unknowns would appear to be largely restricted to factual kinds of knowledge

A detailed study of quasinormal frequencies of the Kerr black hole

We compute the quasinormal frequencies of the Kerr black hole using a continued fraction method. The continued fraction method first proposed by Leaver is still the only known method stable and accurate for the numerical determination of the Kerr quasinormal frequencies. We numerically obtain not only the slowly but also the rapidly damped quasinormal frequencies and analyze the peculiar behavior of these frequencies at the Kerr limit. We also calculate the algebraically special frequency first identified by Chandrasekhar and confirm that it coincide with the $n=8$ quasinormal frequency only at the Schwarzschild limit.Comment: REVTEX, 15 pages, 7 eps figure