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

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

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

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

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

The relation between treasury yields and corporate bond yield spreads

Because the option to call a corporate bond should rise in value when bond yields fall, the relation between noncallable Treasury yields and spreads of corporate bond yields over Treasury yields should depend on the callability of the corporate bond. I confirm this hypothesis for investment-grade corporate bonds. Although yield spreads on both callable and noncallable corporate bonds fall when Treasury yields rise, this relation is much stronger for callable bonds. This result has important implications for interpreting the behavior of yields on commonly used corporate bond indexes, which are composed primarily of callable bonds. COMMONLY USED INDEXES OF CORPORATE bond yields, such as those produced by Moody’s or Lehman Brothers, are constructed using both callable and noncallable bonds. Because the objective of those producing the indexes is to track the universe of corporate bonds, this methodology is sensible. Until the mid-1980s, few corporations issued noncallable bonds, hence an index designed to measure the yield on a typical corporate bond would have to b

The Subgraph Isomorphism Problem on a Class of Hyperedge Replacement Languages

A graph class is called A-free if every graph in the class has no graph in the set A as an induced subgraph. Such characterisations by forbidden induced subgraphs are (among other purposes) very useful for determining whether A-free is a subclass of B-free, by determining whether every graph in B has some graph in A as an induced subgraph. This requires solving the Subgraph Isomorphism Problem, which is NP-complete in general, but for which effective practical algorithms for general and specific purposes exist. However, if B is infinite, these algorithms cannot be used. We introduce Head-Mid-Tail grammars (a special case of hyperedge replacement grammars) which have the property that if an infinite set B can be defined by a Head-Mid-Tail grammar then it is decidable whether every graph in B contains some graph from a finite set A of graphs as an induced subgraph, thereby solving the A-free ⊆ B-free problem. Moreover, our algorithm is both simple and efficient enough to be practical