Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.Comment: 15 page

High-resolution UV spectrum of the benzene—N2 van der Waals complex

The rotationally resolved spectrum of the 610 band of the S1 ← S0 electronic transition of the benzene—N2 van der Waals complex has been recorded and 119 transitions assigned. The C6H6·N2 complex, produced in a pulsed molecular beam, was detected by mass-selected two-photon two-colour ionization employing a high-resolution (ΔνUV = 100 MHz, fwhm) pulsed-amplified cw laser for the resonant intermediate excitation. The observed rotational structure is that of a rigid symmetric top with weaker additional rotational transitions most likely arising from the free internal rotation of the N2 in the plane parallel to the benzene ring. The N2 is located parallel to the benzene ring at a distance of 3.50 Å; this decreases by 45 mÅ in the excited electronic state

Beyond Blobs in Percolation Cluster Structure: The Distribution of 3-Blocks at the Percolation Threshold

The incipient infinite cluster appearing at the bond percolation threshold can be decomposed into singly-connected ``links'' and multiply-connected ``blobs.'' Here we decompose blobs into objects known in graph theory as 3-blocks. A 3-block is a graph that cannot be separated into disconnected subgraphs by cutting the graph at 2 or fewer vertices. Clusters, blobs, and 3-blocks are special cases of $k$-blocks with $k=1$, 2, and 3, respectively. We study bond percolation clusters at the percolation threshold on 2-dimensional square lattices and 3-dimensional cubic lattices and, using Monte-Carlo simulations, determine the distribution of the sizes of the 3-blocks into which the blobs are decomposed. We find that the 3-blocks have fractal dimension $d_3=1.2\pm 0.1$ in 2D and $1.15\pm 0.1$ in 3D. These fractal dimensions are significantly smaller than the fractal dimensions of the blobs, making possible more efficient calculation of percolation properties. Additionally, the closeness of the estimated values for $d_3$ in 2D and 3D is consistent with the possibility that $d_3$ is dimension independent. Generalizing the concept of the backbone, we introduce the concept of a ``$k$-bone'', which is the set of all points in a percolation system connected to $k$ disjoint terminal points (or sets of disjoint terminal points) by $k$ disjoint paths. We argue that the fractal dimension of a $k$-bone is equal to the fractal dimension of $k$-blocks, allowing us to discuss the relation between the fractal dimension of $k$-blocks and recent work on path crossing probabilities.Comment: All but first 2 figs. are low resolution and are best viewed when printe

Measurement Near Threshold of 9-Be(3-He, Pi) to the A = 12 Isobaric Triplet by Recoil Detection

This work was supported by the National Science Foundation Grant NSF PHY 81-14339 and by Indiana Universit

Asymmetry of Strange Sea in Nucleons

Based on the finite-temperature field theory, we evaluate the medium effects in nucleon which can induce an asymmetry between quarks and antiquarks of the strange sea. The short-distance effects determined by the weak interaction can give rise to $\delta m\equiv \Delta m_s-\Delta m_{\bar s}$ where $\Delta m_{s(\bar s)}$ is the medium-induced mass of strange quark by a few KeV at most, but the long-distance effects by strong interaction are sizable. Our numerical results show that there exists an obvious mass difference between strange and anti-strange quarks, as large as 10-100 MeV.Comment: 15 latex pages, 3 figures, to appear in PR

Theoretical analysis of neutron scattering results for quasi-two dimensional ferromagnets

A theoretical study has been carried out to analyse the available results from the inelastic neutron scattering experiment performed on a quasi-two dimensional spin-1/2 ferromagnetic material $K_2CuF_4$. Our formalism is based on a conventional semi-classical like treatment involving a model of an ideal gas of vortices/anti-vortices corresponding to an anisotropic XY Heisenberg ferromagnet on a square lattice. The results for dynamical structure functions for our model corresponding to spin-1/2, show occurrence of negative values in a large range of energy transfer even encompassing the experimental range, when convoluted with a realistic spectral window function. This result indicates failure of the conventional theoretical framework to be applicable to the experimental situation corresponding to low spin systems. A full quantum formalism seems essential for treating such systems.Comment: 16 pages, 6 figures, 1 Table Submitted for publicatio

Climate impact research: Beyond patchwork

Despite significant progress in climate impact research, the narratives that science can presently piece together of a 2, 3, 4, or 5 °C warmer world remain fragmentary. Here we briefly review past undertakings to characterise comprehensively and quantify climate impacts based on multi-model approaches. We then report on the Inter-Sectoral Impact Model Intercomparison Project (ISI-MIP), a community-driven effort to compare impact models across sectors and scales systematically, and to quantify the uncertainties along the chain from greenhouse gas emissions and climate input data to the modelling of climate impacts themselves. We show how ISI-MIP and similar efforts can substantially advance the science relevant to impacts, adaptation and vulnerability, and we outline the steps that need to be taken in order to make the most of the available modelling tools. We discuss pertinent limitations of these methods and how they could be tackled. We argue that it is time to consolidate the current patchwork of impact knowledge through integrated cross-sectoral assessments, and that the climate impact community is now in a favourable position to do so

Climate impact research: Beyond patchwork

Despite significant progress in climate impact research, the narratives that science can presently piece together of a 2, 3, 4, or 5 degrees C warmer world remain fragmentary. Here we briefly review past undertakings to characterise comprehensively and quantify climate impacts based on multi-model approaches. We then report on the Inter-Sectoral Impact Model Intercomparison Project (ISI-MIP), a community-driven effort to compare impact models across sectors and scales systematically, and to quantify the uncertainties along the chain from greenhouse gas emissions and climate input data to the modelling of climate impacts themselves. We show how ISI-MIP and similar efforts can substantially advance the science relevant to impacts, adaptation and vulnerability, and we outline the steps that need to be taken in order to make the most of the available modelling tools. We discuss pertinent limitations of these methods and how they could be tackled. We argue that it is time to consolidate the current patchwork of impact knowledge through integrated cross-sectoral assessments, and that the climate impact community is now in a favourable position to do so

The spectrum of high-energy cosmic rays measured with KASCADE-Grande

The energy spectrum of cosmic rays between 10**16 eV and 10**18 eV, derived from measurements of the shower size (total number of charged particles) and the total muon number of extensive air showers by the KASCADE-Grande experiment, is described. The resulting all-particle energy spectrum exhibits strong hints for a hardening of the spectrum at approximately 2x10**16 eV and a significant steepening at c. 8x10**16 eV. These observations challenge the view that the spectrum is a single power law between knee and ankle. Possible scenarios generating such features are discussed in terms of astrophysical processes that may explain the transition region from galactic to extragalactic origin of cosmic rays.Comment: accepted by Astroparticle Physics June 201