The development of a program analysis environment for Ada

A unit level, Ada software module testing system, called Query Utility Environment for Software Testing of Ada (QUEST/Ada), is described. The project calls for the design and development of a prototype system. QUEST/Ada design began with a definition of the overall system structure and a description of component dependencies. The project team was divided into three groups to resolve the preliminary designs of the parser/scanner: the test data generator, and the test coverage analyzer. The Phase 1 report is a working document from which the system documentation will evolve. It provides history, a guide to report sections, a literature review, the definition of the system structure and high level interfaces, descriptions of the prototype scope, the three major components, and the plan for the remainder of the project. The appendices include specifications, statistics, two papers derived from the current research, a preliminary users' manual, and the proposal and work plan for Phase 2

A Conserved DNA Repeat Promotes Selection of a Diverse Repertoire of Trypanosoma brucei Surface Antigens from the Genomic Archive.

African trypanosomes are mammalian pathogens that must regularly change their protein coat to survive in the host bloodstream. Chronic trypanosome infections are potentiated by their ability to access a deep genomic repertoire of Variant Surface Glycoprotein (VSG) genes and switch from the expression of one VSG to another. Switching VSG expression is largely based in DNA recombination events that result in chromosome translocations between an acceptor site, which houses the actively transcribed VSG, and a donor gene, drawn from an archive of more than 2,000 silent VSGs. One element implicated in these duplicative gene conversion events is a DNA repeat of approximately 70 bp that is found in long regions within each BES and short iterations proximal to VSGs within the silent archive. Early observations showing that 70-bp repeats can be recombination boundaries during VSG switching led to the prediction that VSG-proximal 70-bp repeats provide recombinatorial homology. Yet, this long held assumption had not been tested and no specific function for the conserved 70-bp repeats had been demonstrated. In the present study, the 70-bp repeats were genetically manipulated under conditions that induce gene conversion. In this manner, we demonstrated that 70-bp repeats promote access to archival VSGs. Synthetic repeat DNA sequences were then employed to identify the length, sequence, and directionality of repeat regions required for this activity. In addition, manipulation of the 70-bp repeats allowed us to observe a link between VSG switching and the cell cycle that had not been appreciated. Together these data provide definitive support for the long-standing hypothesis that 70-bp repeats provide recombinatorial homology during switching. Yet, the fact that silent archival VSGs are selected under these conditions suggests the 70-bp repeats also direct DNA pairing and recombination machinery away from the closest homologs (silent BESs) and toward the rest of the archive

Speaking out about gender imbalance in invited speakers improves diversity.

Omissions of qualified women scientists from major meeting programs continue to occur despite a surge in articles indicating persistent gender-discriminatory practices in hiring and promotion, and calls for gender balance in conference organizing committees

Parametric Forcing of Waves with Non-Monotonic Dispersion Relation: Domain Structures in Ferrofluids?

Surface waves on ferrofluids exposed to a dc-magnetic field exhibit a non-monotonic dispersion relation. The effect of a parametric driving on such waves is studied within suitable coupled Ginzburg-Landau equations. Due to the non-monotonicity the neutral curve for the excitation of standing waves can have up to three minima. The stability of the waves with respect to long-wave perturbations is determined $via$ a phase-diffusion equation. It shows that the band of stable wave numbers can split up into two or three sub-bands. The resulting competition between the wave numbers corresponding to the respective sub-bands leads quite naturally to patterns consisting of multiple domains of standing waves which differ in their wave number. The coarsening dynamics of such domain structures is addressed.Comment: 23 pages, 6 postscript figures, composed using RevTeX. Submitted to PR

Scarred Patterns in Surface Waves

Surface wave patterns are investigated experimentally in a system geometry that has become a paradigm of quantum chaos: the stadium billiard. Linear waves in bounded geometries for which classical ray trajectories are chaotic are known to give rise to scarred patterns. Here, we utilize parametrically forced surface waves (Faraday waves), which become progressively nonlinear beyond the wave instability threshold, to investigate the subtle interplay between boundaries and nonlinearity. Only a subset (three main types) of the computed linear modes of the stadium are observed in a systematic scan. These correspond to modes in which the wave amplitudes are strongly enhanced along paths corresponding to certain periodic ray orbits. Many other modes are found to be suppressed, in general agreement with a prediction by Agam and Altshuler based on boundary dissipation and the Lyapunov exponent of the associated orbit. Spatially asymmetric or disordered (but time-independent) patterns are also found even near onset. As the driving acceleration is increased, the time-independent scarred patterns persist, but in some cases transitions between modes are noted. The onset of spatiotemporal chaos at higher forcing amplitude often involves a nonperiodic oscillation between spatially ordered and disordered states. We characterize this phenomenon using the concept of pattern entropy. The rate of change of the patterns is found to be reduced as the state passes temporarily near the ordered configurations of lower entropy. We also report complex but highly symmetric (time-independent) patterns far above onset in the regime that is normally chaotic.Comment: 9 pages, 10 figures (low resolution gif files). Updated and added references and text. For high resolution images: http://physics.clarku.edu/~akudrolli/stadium.htm

Wound-up phase turbulence in the Complex Ginzburg-Landau equation

We consider phase turbulent regimes with nonzero winding number in the one-dimensional Complex Ginzburg-Landau equation. We find that phase turbulent states with winding number larger than a critical one are only transients and decay to states within a range of allowed winding numbers. The analogy with the Eckhaus instability for non-turbulent waves is stressed. The transition from phase to defect turbulence is interpreted as an ergodicity breaking transition which occurs when the range of allowed winding numbers vanishes. We explain the states reached at long times in terms of three basic states, namely quasiperiodic states, frozen turbulence states, and riding turbulence states. Justification and some insight into them is obtained from an analysis of a phase equation for nonzero winding number: rigidly moving solutions of this equation, which correspond to quasiperiodic and frozen turbulence states, are understood in terms of periodic and chaotic solutions of an associated system of ordinary differential equations. A short report of some of our results has been published in [Montagne et al., Phys. Rev. Lett. 77, 267 (1996)].Comment: 22 pages, 15 figures included. Uses subfigure.sty (included) and epsf.tex (not included). Related research in http://www.imedea.uib.es/Nonlinea

Amplitude equations and pattern selection in Faraday waves

We present a systematic nonlinear theory of pattern selection for parametric surface waves (Faraday waves), not restricted to fluids of low viscosity. A standing wave amplitude equation is derived from the Navier-Stokes equations that is of gradient form. The associated Lyapunov function is calculated for different regular patterns to determine the selected pattern near threshold. For fluids of large viscosity, the selected wave pattern consists of parallel stripes. At lower viscosity, patterns of square symmetry are obtained in the capillary regime (large frequencies). At lower frequencies (the mixed gravity-capillary regime), a sequence of six-fold (hexagonal), eight-fold, ... patterns are predicted. The regions of stability of the various patterns are in quantitative agreement with recent experiments conducted in large aspect ratio systems.Comment: 12 pages, 1 figure, Revte