Hydrodynamic turbulence cannot transport angular momentum effectively in astrophysical disks

The most efficient energy sources known in the Universe are accretion disks. Those around black holes convert 5 -- 40 per cent of rest-mass energy to radiation. Like water circling a drain, inflowing mass must lose angular momentum, presumably by vigorous turbulence in disks, which are essentially inviscid. The origin of the turbulence is unclear. Hot disks of electrically conducting plasma can become turbulent by way of the linear magnetorotational instability. Cool disks, such as the planet-forming disks of protostars, may be too poorly ionized for the magnetorotational instability to occur, hence essentially unmagnetized and linearly stable. Nonlinear hydrodynamic instability often occurs in linearly stable flows (for example, pipe flows) at sufficiently large Reynolds numbers. Although planet-forming disks have extreme Reynolds numbers, Keplerian rotation enhances their linear hydrodynamic stability, so the question of whether they can be turbulent and thereby transport angular momentum effectively is controversial. Here we report a laboratory experiment, demonstrating that non-magnetic quasi-Keplerian flows at Reynolds numbers up to millions are essentially steady. Scaled to accretion disks, rates of angular momentum transport lie far below astrophysical requirements. By ruling out purely hydrodynamic turbulence, our results indirectly support the magnetorotational instability as the likely cause of turbulence, even in cool disks.Comment: 12 pages and 4 figures. To be published in Nature on November 16, 2006, available at http://www.nature.com/nature/journal/v444/n7117/abs/nature05323.htm

cPath: open source software for collecting, storing, and querying biological pathways

BACKGROUND: Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. RESULTS: We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. CONCLUSION: cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling