Recycling Information: Science Through Data Mining

An article considering the changes afoot in the world of Science and how the exponentially increasing amounts of recorded data are affecting the way in which scientists now work, for example with data mining. Changes in the way that resources become obsolete are also discussed and how more value must be placed on the work of professionals in digital curation

Linking to Linked Data

Does very precise description of objects and semantic-web linking truly enable new applications for catalog data? This poster presents research testing this questions using data from a variety of library, museum and archive collections.ye

The eta' meson from lattice QCD

We study the flavour singlet pseudoscalar mesons from first principles using lattice QCD. With N_f=2 flavours of light quark, this is the so-called eta_2 meson and we discuss the phenomenological status of this. Using maximally twisted-mass lattice QCD, we extract the mass of the eta_2 meson at two values of the lattice spacing for lighter quarks than previously discussed in the literature. We are able to estimate the mass value in the limit of light quarks with their physical masses.Comment: 16 pages: version accepted for publicatio

Flavor Singlet Meson Mass in the Continuum Limit in Two-Flavor Lattice QCD

We present results for the mass of the eta-prime meson in the continuum limit for two-flavor lattice QCD, calculated on the CP-PACS computer, using a renormalization-group improved gauge action, and Sheikholeslami and Wohlert's fermion action with tadpole-improved csw. Correlation functions are measured at three values of the coupling constant beta corresponding to the lattice spacing a approx. 0.22, 0.16, 0.11 fm and for four values of the quark mass parameter kappa corresponding to mpi over mrho approx. 0.8, 0.75, 0.7 and 0.6. For each beta, kappa pair, 400-800 gauge configurations are used. The two-loop diagrams are evaluated using a noisy source method. We calculate eta-prime propagators using local sources, and find that excited state contributions are much reduced by smearing. A full analysis for the smeared propagators gives metaprime=0.960(87)+0.036-0.248 GeV, in the continuum limit, where the second error represents the systematic uncertainty coming from varying the functional form for chiral and continuum extrapolations.Comment: 9 pages, 19 figures, 4 table

Thermodynamics of SU(3) gauge theory on anisotropic lattices

Finite temperature SU(3) gauge theory is studied on anisotropic lattices using the standard plaquette gauge action. The equation of state is calculated on $16^{3} \times 8$, $20^{3} \times 10$ and $24^{3} \times 12$ lattices with the anisotropy $\xi \equiv a_s / a_t = 2$, where $a_s$ and $a_t$ are the spatial and temporal lattice spacings. Unlike the case of the isotropic lattice on which $N_t=4$ data deviate significantly from the leading scaling behavior, the pressure and energy density on an anisotropic lattice are found to satisfy well the leading $1/N_t^2$ scaling from our coarsest lattice, $N_t/\xi=4$. With three data points at $N_t/\xi=4$, 5 and 6, we perform a well controlled continuum extrapolation of the equation of state. Our results in the continuum limit agree with a previous result from isotropic lattices using the same action, but have smaller and more reliable errors.Comment: RevTeX, 21 pages, 17 PS figures. A quantitative test about the benefit of anisotropic lattices added, minor errors corrected. Final version for PR

Robust probabilistic superposition and comparison of protein structures

<p>Abstract</p> <p>Background</p> <p>Protein structure comparison is a central issue in structural bioinformatics. The standard dissimilarity measure for protein structures is the root mean square deviation (RMSD) of representative atom positions such as α-carbons. To evaluate the RMSD the structures under comparison must be superimposed optimally so as to minimize the RMSD. How to evaluate optimal fits becomes a matter of debate, if the structures contain regions which differ largely - a situation encountered in NMR ensembles and proteins undergoing large-scale conformational transitions.</p> <p>Results</p> <p>We present a probabilistic method for robust superposition and comparison of protein structures. Our method aims to identify the largest structurally invariant core. To do so, we model non-rigid displacements in protein structures with outlier-tolerant probability distributions. These distributions exhibit heavier tails than the Gaussian distribution underlying standard RMSD minimization and thus accommodate highly divergent structural regions. The drawback is that under a heavy-tailed model analytical expressions for the optimal superposition no longer exist. To circumvent this problem we work with a scale mixture representation, which implies a weighted RMSD. We develop two iterative procedures, an Expectation Maximization algorithm and a Gibbs sampler, to estimate the local weights, the optimal superposition, and the parameters of the heavy-tailed distribution. Applications demonstrate that heavy-tailed models capture differences between structures undergoing substantial conformational changes and can be used to assess the precision of NMR structures. By comparing Bayes factors we can automatically choose the most adequate model. Therefore our method is parameter-free.</p> <p>Conclusions</p> <p>Heavy-tailed distributions are well-suited to describe large-scale conformational differences in protein structures. A scale mixture representation facilitates the fitting of these distributions and enables outlier-tolerant superposition.</p

Theta dependence of SU(N) gauge theories in the presence of a topological term

We review results concerning the theta dependence of 4D SU(N) gauge theories and QCD, where theta is the coefficient of the CP-violating topological term in the Lagrangian. In particular, we discuss theta dependence in the large-N limit. Most results have been obtained within the lattice formulation of the theory via numerical simulations, which allow to investigate the theta dependence of the ground-state energy and the spectrum around theta=0 by determining the moments of the topological charge distribution, and their correlations with other observables. We discuss the various methods which have been employed to determine the topological susceptibility, and higher-order terms of the theta expansion. We review results at zero and finite temperature. We show that the results support the scenario obtained by general large-N scaling arguments, and in particular the Witten-Veneziano mechanism to explain the U(1)_A problem. We also compare with results obtained by other approaches, especially in the large-N limit, where the issue has been also addressed using, for example, the AdS/CFT correspondence. We discuss issues related to theta dependence in full QCD: the neutron electric dipole moment, the dependence of the topological susceptibility on the quark masses, the U(1)_A symmetry breaking at finite temperature. We also consider the 2D CP(N) model, which is an interesting theoretical laboratory to study issues related to topology. We review analytical results in the large-N limit, and numerical results within its lattice formulation. Finally, we discuss the main features of the two-point correlation function of the topological charge density.Comment: A typo in Eq. (3.9) has been corrected. An additional subsection (5.2) has been inserted to demonstrate the nonrenormalizability of the relevant theta parameter in the presence of massive fermions, which implies that the continuum (a -> 0) limit must be taken keeping theta fixe