Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Tuning electronic structures via epitaxial strain in Sr2IrO4 thin films

We have synthesized epitaxial Sr2IrO4 thin-films on various substrates and studied their electronic structures as a function of lattice-strains. Under tensile (compressive) strains, increased (decreased) Ir-O-Ir bond-angles are expected to result in increased (decreased) electronic bandwidths. However, we have observed that the two optical absorption peaks near 0.5 eV and 1.0 eV are shifted to higher (lower) energies under tensile (compressive) strains, indicating that the electronic-correlation energy is also affected by in-plane lattice-strains. The effective tuning of electronic structures under lattice-modification provides an important insight into the physics driven by the coexisting strong spin-orbit coupling and electronic correlation.Comment: 9 pages, 5 figures, 1 tabl

Note on SLE and logarithmic CFT

It is discussed how stochastic evolutions may be linked to logarithmic conformal field theory. This introduces an extension of the stochastic Loewner evolutions. Based on the existence of a logarithmic null vector in an indecomposable highest-weight module of the Virasoro algebra, the representation theory of the logarithmic conformal field theory is related to entities conserved in mean under the stochastic process.Comment: 10 pages, LaTeX, v2: version to be publishe

Great Expectations: Voluntary Sports Clubs and Their Role in Delivering National Policy for English Sport

“The original publication is available at www.springerlink.com”. Copyright International Society for Third-Sector Research and The Johns Hopkins University. DOI: 10.1007/s11266-009-9095-yVoluntary sports clubs (VSCs) account for about a quarter of all volunteering in England. The volunteers work in a mutual aid, self-production, self-consumption system whose main purpose is identifying and nurturing high-level performers. But the new HMG/Sport England strategies leading to London 2012 expects volunteers to make a major contribution to sustaining and extending participation. The study utilized six focus group sessions with a total of 36 officials and members of 36 clubs across the six counties of Eastern England to assess whether and to what extent government policy objectives can be delivered through the voluntary sector. The study focused on the perceptions and attitudes of club members about being expected to serve public policy and the current pressures they and their clubs face. The results lead the authors to question the appropriateness, sensitivity, and feasibility of current sport policy, particularly the emphasis on VSCs as policy implementers.Peer reviewe

Proposal for a CFT interpretation of Watts' differential equation for percolation

G. M. T. Watts derived that in two dimensional critical percolation the crossing probability Pi_hv satisfies a fifth order differential equation which includes another one of third order whose independent solutions describe the physically relevant quantities 1, Pi_h, Pi_hv. We will show that this differential equation can be derived from a level three null vector condition of a rational c=-24 CFT and motivate how this solution may be fitted into known properties of percolation.Comment: LaTeX, 20p, added references, corrected typos and additional content

Non-diagonal open spin-1/2 XXZ quantum chains by separation of variables: Complete spectrum and matrix elements of some quasi-local operators

The integrable quantum models, associated to the transfer matrices of the 6-vertex reflection algebra for spin 1/2 representations, are studied in this paper. In the framework of Sklyanin's quantum separation of variables (SOV), we provide the complete characterization of the eigenvalues and eigenstates of the transfer matrix and the proof of the simplicity of the transfer matrix spectrum. Moreover, we use these integrable quantum models as further key examples for which to develop a method in the SOV framework to compute matrix elements of local operators. This method has been introduced first in [1] and then used also in [2], it is based on the resolution of the quantum inverse problem (i.e. the reconstruction of all local operators in terms of the quantum separate variables) plus the computation of the action of separate covectors on separate vectors. In particular, for these integrable quantum models, which in the homogeneous limit reproduce the open spin-1/2 XXZ quantum chains with non-diagonal boundary conditions, we have obtained the SOV-reconstructions for a class of quasi-local operators and determinant formulae for the covector-vector actions. As consequence of these findings we provide one determinant formulae for the matrix elements of this class of reconstructed quasi-local operators on transfer matrix eigenstates.Comment: 40 pages. Minor modifications in the text and some notations and some more reference adde

The open XXZ and associated models at q root of unity

The generalized open XXZ model at $q$ root of unity is considered. We review how associated models, such as the $q$ harmonic oscillator, and the lattice sine-Gordon and Liouville models are obtained. Explicit expressions of the local Hamiltonian of the spin ${1 \over 2}$ XXZ spin chain coupled to dynamical degrees of freedom at the one end of the chain are provided. Furthermore, the boundary non-local charges are given for the lattice sine Gordon model and the $q$ harmonic oscillator with open boundaries. We then identify the spectrum and the corresponding Bethe states, of the XXZ and the q harmonic oscillator in the cyclic representation with special non diagonal boundary conditions. Moreover, the spectrum and Bethe states of the lattice versions of the sine-Gordon and Liouville models with open diagonal boundaries is examined. The role of the conserved quantities (boundary non-local charges) in the derivation of the spectrum is also discussed.Comment: 31 pages, LATEX, minor typos correcte