Shearing box simulations of accretion disk winds

The launching process of a magnetically driven outflow from an accretion disk is investigated in a local, shearing box model which allows a study of the feedback between accretion and angular momentum loss. The mass-flux instability found in previous linear analyses of this problem is recovered in a series of 2D (axisymmetric) simulations in the MRI-stable (high magnetic field strength) regime. At low field strengths that are still sufficient to suppress MRI, the instability develops on a short radial length scale and saturates at a modest amplitude. At high field strengths, a long-wavelength "clump" instability of large amplitude is observed, with growth times of a few orbits. As speculated before, the unstable connection between disk and outflow may be relevant for the time dependence observed in jet-producing disks. The success of the simulations is due in a large part to the implementation of an effective wave-transmitting upper boundary condition.Comment: 10 pages, 13 figure, accepted for publication in A&A, complimentary movies at http://ucolick.org/~rainer/pascheibe

LabelHash: A Flexible and Extensible Method for Matching Structural Motifs

There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Below, we will briefly describe LabelHash, a new method for partial structure comparison. In partial structure comparison, the goal is to find the best geometric and chemical similarity between a set of 3D points called a _motif_ and a subset of a set of 3D points called the _target_. Both the motif and targets are represented as sets of labeled 3D points. A motif is ideally composed of the functionally most-relevant residues in a binding site. The labels denote the type of residue. Motif points can have multiple labels to denote that substitutions are allowed. Any subset of the target that has labels that are compatible with the motif’s labels is called a _match_. The aim is to find statistically significant matches to a structural motif. Our method preprocesses a background database of targets such as a non-redundant subset of the Protein Data Bank in such a way that we can look up in constant time partial matches to a motif. Using a variant of the previously described match augmentation algorithm (1), we obtain complete matches to our motif. The nonparametric statistical model developed by (2,3) corrects for any bias introduced by our algorithm. This bias is introduced by excluding matches that do not satisfy certain geometric constraints for efficiency reasons

Rational Landen transformations on the real line

The rational Landen transformation is a map on the space of coefficients of a rational integrand that preserves the value of the integral. We provide a family of these transformations that apply to rational integrands on the whole line. Given an integer m, these transformations produce a numerical scheme to evaluate the integral that is of order m.Comment: 22 page