Equations, inequations and inequalities characterizing the configurations of two real projective conics

Couples of proper, non-empty real projective conics can be classified modulo rigid isotopy and ambient isotopy. We characterize the classes by equations, inequations and inequalities in the coefficients of the quadratic forms defining the conics. The results are well--adapted to the study of the relative position of two conics defined by equations depending on parameters.Comment: 31 pages. See also http://emmanuel.jean.briand.free.fr/publications/twoconics/ Added references to important prior work on the subject. The title changed accordingly. Some typos and imprecisions corrected. To be published in Applicable Algebra in Engineering, Communication and Computin

Topological Mixing with Ghost Rods

Topological chaos relies on the periodic motion of obstacles in a two-dimensional flow in order to form nontrivial braids. This motion generates exponential stretching of material lines, and hence efficient mixing. Boyland et al. [P. L. Boyland, H. Aref, and M. A. Stremler, J. Fluid Mech. 403, 277 (2000)] have studied a specific periodic motion of rods that exhibits topological chaos in a viscous fluid. We show that it is possible to extend their work to cases where the motion of the stirring rods is topologically trivial by considering the dynamics of special periodic points that we call ghost rods, because they play a similar role to stirring rods. The ghost rods framework provides a new technique for quantifying chaos and gives insight into the mechanisms that produce chaos and mixing. Numerical simulations for Stokes flow support our results.Comment: 13 pages, 11 figures. RevTeX4 format. (Final version

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize the solutions to the corresponding tangle equations by certain knotted graphs. By investigating planarity conditions on these graphs we show that there is a unique biologically relevant solution. That is, we show there is a unique rational tangle solution, which is also the unique solution with small crossing number.Comment: 60 pages, 74 figure