E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

Can the magnetic moment contribution explain the A_y puzzle?

We evaluate the full one-photon-exchange Born amplitude for $Nd$ scattering. We include the contributions due to the magnetic moment of the proton or neutron, and the magnetic moment and quadrupole moment of the deuteron. It is found that the inclusion of the magnetic-moment interaction in the theoretical description of the $Nd$ scattering observables cannot resolve the long-standing $A_y$ puzzle.Comment: 7 pages, 2 Postscript figures; to appear in Phys.Rev.

Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example

BACKGROUND: A complete gene-expression microarray should preferably detect all genomic sequences that can be expressed as RNA in an organism, i.e. the transcriptome. However, our knowledge of a transcriptome of any organism still is incomplete and transcriptome information is continuously being updated. Here, we present a strategy to integrate heterogeneous sequence information that can be used as input for an up-to-date microarray design. FINDINGS: Our algorithm consists of four steps. In the first step transcripts from different resources are grouped into Transcription Clusters (TCs) by looking at the similarity of all transcripts. TCs are groups of transcripts with a similar length. If a transcript is much smaller than a TC to which it is highly similar, it will be annotated as a subsequence of that TC and is used for probe design only if the probe designed for the TC does not query the subsequence. Secondly, all TCs are mapped to a genome assembly and gene information is added to the design. Thirdly TC members are ranked according to their trustworthiness and the most reliable sequence is used for the probe design. The last step is the actual array design. We have used this strategy to build an up-to-date zebrafish microarray. CONCLUSIONS: With our strategy and the software developed, it is possible to use a set of heterogeneous transcript resources for microarray design, reduce the number of candidate target sequences on which the design is based and reduce redundancy. By changing the parameters in the procedure it is possible to control the similarity within the TCs and thus the amount of candidate sequences for the design. The annotation of the microarray is carried out simultaneously with the design

2s Hyperfine Structure in Hydrogen Atom and Helium-3 Ion

The usefulness of study of hyperfine splitting in the hydrogen atom is limited on a level of 10 ppm by our knowledge of the proton structure. One way to go beyond 10 ppm is to study a specific difference of the hyperfine structure intervals 8 Delta nu_2 - Delta nu_1. Nuclear effects for are not important this difference and it is of use to study higher-order QED corrections.Comment: 10 pages, presented at Hydrogen Atom II meeting (2000

Long Range Magnetic Order and the Darwin Lagrangian

We simulate a finite system of $N$ confined electrons with inclusion of the Darwin magnetic interaction in two- and three-dimensions. The lowest energy states are located using the steepest descent quenching adapted for velocity dependent potentials. Below a critical density the ground state is a static Wigner lattice. For supercritical density the ground state has a non-zero kinetic energy. The critical density decreases with $N$ for exponential confinement but not for harmonic confinement. The lowest energy state also depends on the confinement and dimension: an antiferromagnetic cluster forms for harmonic confinement in two dimensions.Comment: 5 figure

Irreversible quantum graphs

Irreversibility is introduced to quantum graphs by coupling the graphs to a bath of harmonic oscillators. The interaction which is linear in the harmonic oscillator amplitudes is localized at the vertices. It is shown that for sufficiently strong coupling, the spectrum of the system admits a new continuum mode which exists even if the graph is compact, and a {\it single} harmonic oscillator is coupled to it. This mechanism is shown to imply that the quantum dynamics is irreversible. Moreover, it demonstrates the surprising result that irreversibility can be introduced by a "bath" which consists of a {\it single} harmonic oscillator

Role of Present and Future Atomic Parity Violation Experiments in Precision Electroweak Tests

Recent reanalyses of the atomic physics effects on the weak charge in cesium have led to a value in much closer agreement with predictions of the Standard Model. We review precision electroweak tests, their implications for upper bounds on the mass of the Higgs boson, possible ways in which these bounds may be circumvented, and the requirements placed upon accuracy of future atomic parity violation experiments by these considerations.Comment: 10 pages, LaTeX, 1 figure, to be submitted to Physical Review D, new data on neutrino deep inelastic scattering include

One- and two-proton transfer reactions with vibrational Nuclei

We extend a semiclassical model of transfer reactions to the case in which one of the collision partners is a vibrational nucleus. The model is applied to one- and two-proton stripping reactions in the 37Cl + 98Mo system, for which a rapid transition from normal to anomalous slope in the two proton transfer reaction at energies around the Coulomb barrier is experimentally observed. This behavior is satisfactorily reproduced by the present extension of the model.Comment: LaTeX, 10 pages, 1 figure (PostScript