Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance

We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can have the same label. Unlike most previous phylogenetic methods using gene trees, this method does not assume that gene tree incongruence is caused by a single, specific biological process, such as gene duplication and loss, deep coalescence, or lateral gene transfer. We prove that it is NP-hard to compute the RF distance between two mul-trees, but it is easy to calculate the generalized RF distance between a mul-tree and a singly-labeled tree. Motivated by this observation, we formulate the RF supertree problem for mul-trees (MulRF), which takes a collection of mul-trees and constructs a species tree that minimizes the total RF distance from the input mul-trees. We present a fast heuristic algorithm for the MulRF supertree problem. Simulation experiments demonstrate that the MulRF method produces more accurate species trees than gene tree parsimony methods when incongruence is caused by gene tree error, duplications and losses, and/or lateral gene transfer. Furthermore, the MulRF heuristic runs quickly on data sets containing hundreds of trees with up to a hundred taxa.Comment: 16 pages, 11 figure

Conservatism implications of shock test tailoring for multiple design environments

A method for analyzing shock conservation in test specifications that have been tailored to qualify a structure for multiple design environments is discussed. Shock test conservation is qualified for shock response spectra, shock intensity spectra and ranked peak acceleration data in terms of an Index of Conservation (IOC) and an Overtest Factor (OTF). The multi-environment conservation analysis addresses the issue of both absolute and average conservation. The method is demonstrated in a case where four laboratory tests have been specified to qualify a component which must survive seven different field environments. Final judgment of the tailored test specification is shown to require an understanding of the predominant failure modes of the test item

Quantum Phase Transition in the Itinerant Antiferromagnet (V0.9Ti0.1)2O3

Quantum-critical behavior of the itinerant electron antiferromagnet (V0.9Ti0.1)2O3 has been studied by single-crystal neutron scattering. By directly observing antiferromagnetic spin fluctuations in the paramagnetic phase, we have shown that the characteristic energy depends on temperature as c_1 + c_2 T^{3/2}, where c_1 and c_2 are constants. This T^{3/2} dependence demonstrates that the present strongly correlated d-electron antiferromagnet clearly shows the criticality of the spin-density-wave quantum phase transition in three space dimensions.Comment: 4 pages, 4 figure

Magnetic Interaction in the Geometrically Frustrated Triangular Lattice Antiferromagnet CuFeO2\rm CuFeO_2

The spin wave excitations of the geometrically frustrated triangular lattice antiferromagnet (TLA) $\rm CuFeO_2$ have been measured using high resolution inelastic neutron scattering. Antiferromagnetic interactions up to third nearest neighbors in the ab plane (J_1, J_2, J_3, with $J_2/J_1 \approx 0.44$ and $J_3/J_1 \approx 0.57$), as well as out-of-plane coupling (J_z, with $J_z/J_1 \approx 0.29$) are required to describe the spin wave dispersion relations, indicating a three dimensional character of the magnetic interactions. Two energy dips in the spin wave dispersion occur at the incommensurate wavevectors associated with multiferroic phase, and can be interpreted as dynamic precursors to the magnetoelectric behavior in this system.Comment: 4 pages, 4 figures, published in Phys. Rev. Let

Magnons in Ferromagnetic Metallic Manganites

Ferromagnetic (FM) manganites, a group of likely half-metallic oxides, are of special interest not only because they are a testing ground of the classical doubleexchange interaction mechanism for the colossal magnetoresistance, but also because they exhibit an extraordinary arena of emergent phenomena. These emergent phenomena are related to the complexity associated with strong interplay between charge, spin, orbital, and lattice. In this review, we focus on the use of inelastic neutron scattering to study the spin dynamics, mainly the magnon excitations in this class of FM metallic materials. In particular, we discussed the unusual magnon softening and damping near the Brillouin zone boundary in relatively narrow band compounds with strong Jahn-Teller lattice distortion and charge/orbital correlations. The anomalous behaviors of magnons in these compounds indicate the likelihood of cooperative excitations involving spin, lattice, as well as orbital degrees of freedom.Comment: published in J. Phys.: Cond. Matt. 20 figure