Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Vortex pinning in high-Tc materials via randomly oriented columnar defects, created by GeV proton-induced fission fragments

Extensive work has shown that irradiation with 0.8 GeV protons can produce randomly oriented columnar defects (CD's) in a large number of HTS materials, specifically those cuprates containing Hg, Tl, Pb, Bi, and similar heavy elements. Absorbing the incident proton causes the nucleus of these species to fission, and the recoiling fission fragments create amorphous tracks, i.e., CD's. The superconductive transition temperature Tc decreases linearly with proton fluence and we analyze how the rate depends on the family of superconductors. In a study of Tl-2212 materials, adding defects decreases the equilibrium magnetization Meq(H) significantly in magnitude and changes its field dependence; this result is modeled in terms of vortex pinning. Analysis of the irreversible magnetization and its time dependence shows marked increases in the persistent current density and effective pinning energy, and leads to an estimate for the elementary attempt time for vortex hopping, tau ~ 4x10^(-9) s.Comment: Submitted to Physica C; presentation at ISS-2001. PDF file only, 13 pp. tota

Global Inverse Consistency for Interactive Constraint Satisfaction

International audienceSome applications require the interactive resolution of a constraint problem by a human user. In such cases, it is highly desirable that the person who interactively solves the problem is not given the choice to select values that do not lead to solutions. We call this property global inverse consistency. Existing systems simulate this either by maintaining arc consistency after each assignment performed by the user or by compiling offline the problem as a multi-valued decision diagram. In this paper, we define several questions related to global inverse consistency and analyse their complexity. Despite their theoretical intractability, we propose several algorithms for enforcing global inverse consistency and we show that the best version is efficient enough to be used in an interactive setting on several configuration and design problems. We finally extend our contribution to the inverse consistency of tuples

Observation of Scaling Violations in Scaled Momentum Distributions at HERA

Charged particle production has been measured in deep inelastic scattering (DIS) events over a large range of $x$ and $Q^2$ using the ZEUS detector. The evolution of the scaled momentum, $x_p$, with $Q^2,$ in the range 10 to 1280 $GeV^2$, has been investigated in the current fragmentation region of the Breit frame. The results show clear evidence, in a single experiment, for scaling violations in scaled momenta as a function of $Q^2$.Comment: 21 pages including 4 figures, to be published in Physics Letters B. Two references adde

D* Production in Deep Inelastic Scattering at HERA

This paper presents measurements of D^{*\pm} production in deep inelastic scattering from collisions between 27.5 GeV positrons and 820 GeV protons. The data have been taken with the ZEUS detector at HERA. The decay channel $D^{*+}\to (D^0 \to K^- \pi^+) \pi^+$ (+ c.c.) has been used in the study. The $e^+p$ cross section for inclusive D^{*\pm} production with $5<Q^2<100 GeV^2$ and $y<0.7$ is 5.3 \pms 1.0 \pms 0.8 nb in the kinematic region {$1.3<p_T(D^{*\pm})<9.0$ GeV and $| \eta(D^{*\pm}) |<1.5$}. Differential cross sections as functions of p_T(D^{*\pm}), $\eta(D^{*\pm}), W$ and $Q^2$ are compared with next-to-leading order QCD calculations based on the photon-gluon fusion production mechanism. After an extrapolation of the cross section to the full kinematic region in p_T(D^{*\pm}) and $\eta$(D^{*\pm}), the charm contribution $F_2^{c\bar{c}}(x,Q^2)$ to the proton structure function is determined for Bjorken $x$ between 2 $\cdot$ 10$^{-4}$ and 5 $\cdot$ 10$^{-3}$.Comment: 17 pages including 4 figure

Measurement of the reaction γ∗p→ϕp\gamma^*p \rightarrow \phi p in deep inelastic e+pe^+p scattering at HERA

The production of phi mesons in the reaction e(+)p --> e(+)phi p (phi --> K+K-), for 7 phi p cross section rises strongly with W. This behaviour is similar to that previously found for the gamma*p --> rho(0)p cross section. This strong dependence cannot be explained by production through soft pomeron exchange, It is, however, consistent with perturbative QCD expectations, where it reflects the rise of the gluon momentum density in the proton at small x. The ratio of sigma(phi)/sigma(rho(0)), which has previously been determined by ZEUS to be 0.065 +/- 0.013 (stat.) in photoproduction at a mean W of 70 GeV, is measured to be 0.18 +/- 0.05 (stat.) +/- 0.03 (syst.) at a mean Q(2) of 12.3 GeV2 and mean W of approximate to 100 GeV and is thus approaching at large Q(2) the value of 2/9 predicted from the quark charges of the vector mesons and a flavour independent production mechanism

Observation of Events with an Energetic Forward Neutron in Deep Inelastic Scattering at HERA

In deep inelastic neutral current scattering of positrons and protons at the center of mass energy of 300 GeV, we observe, with the ZEUS detector, events with a high energy neutron produced at very small scattering angles with respect to the proton direction. The events constitute a fixed fraction of the deep inelastic, neutral current event sample independent of Bjorken x and Q2 in the range 3 · 10-4 \u3c xBJ \u3c 6 · 10-3 and 10 \u3c Q2 \u3c 100 GeV2

Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database