Fast Structural Search in Phylogenetic Databases

As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P. The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

Memory difference control of unknown unstable fixed points: Drifting parameter conditions and delayed measurement

Difference control schemes for controlling unstable fixed points become important if the exact position of the fixed point is unavailable or moving due to drifting parameters. We propose a memory difference control method for stabilization of a priori unknown unstable fixed points by introducing a memory term. If the amplitude of the control applied in the previous time step is added to the present control signal, fixed points with arbitrary Lyapunov numbers can be controlled. This method is also extended to compensate arbitrary time steps of measurement delay. We show that our method stabilizes orbits of the Chua circuit where ordinary difference control fails.Comment: 5 pages, 8 figures. See also chao-dyn/9810029 (Phys. Rev. E 70, 056225) and nlin.CD/0204031 (Phys. Rev. E 70, 046205

Direct path from microscopic mechanics to Debye shielding, Landau damping, and wave-particle interaction

The derivation of Debye shielding and Landau damping from the $N$-body description of plasmas is performed directly by using Newton's second law for the $N$-body system. This is done in a few steps with elementary calculations using standard tools of calculus, and no probabilistic setting. Unexpectedly, Debye shielding is encountered together with Landau damping. This approach is shown to be justified in the one-dimensional case when the number of particles in a Debye sphere becomes large. The theory is extended to accommodate a correct description of trapping and chaos due to Langmuir waves. Shielding and collisional transport are found to be two related aspects of the repulsive deflections of electrons, in such a way that each particle is shielded by all other ones while keeping in uninterrupted motion.Comment: arXiv admin note: substantial text overlap with arXiv:1310.3096, arXiv:1210.154