Reconstructing (super)trees from data sets with missing distances: Not all is lost

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, present significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for datasets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial datasets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for datasets of all sizes, including large datasets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological datasets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso's ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial datasets

Coherent Acoustic Perturbation of Second-Harmonic-Generation in NiO

We investigate the structural and magnetic origins of the unusual ultrafast second-harmonicgeneration (SHG) response of femtosecond-laser-excited nickel oxide (NiO) previously attributed to oscillatory reorientation dynamics of the magnetic structure induced by d-d excitations. Using time-resolved x-ray diffraction from the (3/2 3/2 3/2) magnetic planes, we show that changes in the magnitude of the magnetic structure factor following ultrafast optical excitation are limited to $\Delta/$ = 1.5% in the first 30 ps. An extended investigation of the ultrafast SHG response reveals a strong dependence on wavelength as well as characteristic echoes, both of which give evidence for an acoustic origin of the dynamics. We therefore propose an alternative mechanism for the SHG response based on perturbations of the nonlinear susceptibility via optically induced strain in a spatially confined medium. In this model, the two observed oscillation periods can be understood as the times required for an acoustic strain wave to traverse one coherence length of the SHG process in either the collinear or anti-collinear geometries.Comment: 26 pages, 7 figure

High temperature thermal conductivity of 2-leg spin-1/2 ladders

Based on numerical simulations, a study of the high temperature, finite frequency, thermal conductivity $\kappa(\omega)$ of spin-1/2 ladders is presented. The exact diagonalization and a novel Lanczos technique are employed.The conductivity spectra, analyzed as a function of rung coupling, point to a non-diverging $dc-$limit but to an unconventional low frequency behavior. The results are discussed with perspective recent experiments indicating a significant magnetic contribution to the energy transport in quasi-one dimensional compounds.Comment: 4 pages, 4 figure

Long time scale molecular dynamics using least action

We present here an efficient method for evaluating molecular trajectories over long time scales. The method is based on optimisation of the path action defined by classical mechanics. We test the technique on non-trivial examples drawn from the literature and discuss the effectiveness of this approach in the study of molecular processes. Many of the present techniques for calculating molecular trajectories are limited computationally. Standard forward integration of Newton's equations of motion yields accurate results for a range of systems whose transition times are many orders of magnitude less than most biologically interesting processes. If one wants to extend these calculations to biologically relevant time scales, it is necessary to develop methodologies which avoid this limitation. The process outlined in this paper has been tested on simple systems using harmonic and Lennard--Jones potential energy functions. The algorithm yields stable trajectories and is adjustable to suite available computational resources. In theory, this algorithm is applicable to any molecular system where the initial and final states are known. This could include investigation of chemical reactions, ligand/receptor binding and work cycles of molecular machinery

Recent developments in radiative B decays

We report on recent theoretical progress in radiative B decays. We focus on a calculation of logarithmically enhanced QED corrections to the branching ratio and forward-backward asymmetry in the inclusive rare decay anti-B --> X(s) l+ l-, and present the results of a detailed phenomenological analysis. We also report on the calculation of NNLO QCD corrections to the inclusive decay anti-B --> X(s) gamma. As far as exclusive modes are concerned we consider transversity amplitudes and the impact of right-handed currents in the exclusive anti-B --> K^* l+ l- decay. Finally, we state results for exclusive B --> V gamma decays, notably the time-dependent CP-asymmetry in the exclusive B --> K^* gamma decay and its potential to serve as a so-called ``null test'' of the Standard Model, and the extraction of CKM and unitarity triangle parameters from B --> (rho,omega) gamma and B --> K^* gamma decays.Comment: 5 pages, 2 figures. Accepted for publication in the proceedings of International Europhysics Conference on High Energy Physics (EPS-HEP2007), Manchester, England, 19-25 Jul 200

R2D2 - a symmetric measurement of reactor neutrinos free of systematical errors

We discuss a symmetric setup for a reactor neutrino oscillation experiment consisting of two reactors separated by about 1 km, and two symmetrically placed detectors, one close to each reactor. We show that such a configuration allows a determination of $\sin^22\theta_{13}$ which is essentially free of systematical errors, if it is possible to separate the contributions of the two reactors in each detector sufficiently. This can be achieved either by considering data when in an alternating way only one reactor is running or by directional sensitivity obtained from the neutron displacement in the detector.Comment: 11 pages, 3 figures, clarifications added, some numbers in relation with the neutron displacement corrected, version to appear in JHE