Fast Arc-Annotated Subsequence Matching in Linear Space

An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$ can be obtained from $Q$ by deleting bases from $Q$. Whenever a base is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are ``nested'' are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using $O(nm)$ time and space, where $m$ and $n$ are the lengths of $P$ and $Q$, respectively. In this paper we present a new algorithm using $O(nm)$ time and $O(n + m)$ space, thereby matching the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc-annotated strings.Comment: To appear in Algoritmic

Structure of Pion Photoproduction Amplitudes

We derive and apply the finite energy sum rules to pion photoproduction. We evaluate the low energy part of the sum rules using several state-of-the-art models. We show how the differences in the low energy side of the sum rules might originate from different quantum number assignments of baryon resonances. We interpret the observed features in the low energy side of the sum rules with the expectation from Regge theory. Finally, we present a model, in terms of a Regge-pole expansion, that matches the sum rules and the high-energy observables.Comment: 19 pages, 15 figures and 4 table

Dispersion and uncertainty in multislit matter wave diffraction

We show that single and multislit experiments involving matter waves may be constructed to assess correlations between the position and momentum of a single free particle. These correlations give rise to position dependent phases which develop dynamically and may play an important role in the interference patterns. For large enough transverse coherence lenght such interference patterns are noticeably different from those of a classical dispersion free wave.Comment: 7 pages, 5 figures, revised manuscrip

The zero exemplar distance problem

Given two genomes with duplicate genes, \textsc{Zero Exemplar Distance} is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome. Blin, Fertin, Sikora, and Vialette recently proved that \textsc{Zero Exemplar Distance} for monochromosomal genomes is NP-hard even if each gene appears at most two times in each genome, thereby settling an important open question on genome rearrangement in the exemplar model. In this paper, we give a very simple alternative proof of this result. We also study the problem \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order, and prove the analogous result that it is also NP-hard even if each gene appears at most two times in each genome. For the positive direction, we show that both variants of \textsc{Zero Exemplar Distance} admit polynomial-time algorithms if each gene appears exactly once in one genome and at least once in the other genome. In addition, we present a polynomial-time algorithm for the related problem \textsc{Exemplar Longest Common Subsequence} in the special case that each mandatory symbol appears exactly once in one input sequence and at least once in the other input sequence. This answers an open question of Bonizzoni et al. We also show that \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order is fixed-parameter tractable if the parameter is the maximum number of chromosomes in each genome.Comment: Strengthened and reorganize

Strong and Radiative Meson Decays in a Generalized Nambu--Jona-Lasinio Model

We investigate strong and radiative meson decays in a generalized Nambu--Jona-Lasinio model. The one loop order calculation provides a satisfactory agreement with the data for the mesonic spectrum and for radiative decays. Higher order effects for strong decays of $\rho$ and $K^*$ are estimated to be large. We also discuss the role of the flavour mixing determinantal interaction.Comment: 7 pages, LaTeX, 2 figs available upon request, CRN 92-4

Thermodynamic potential with correct asymptotics for PNJL model

An attempt is made to resolve certain incongruities within the Nambu - Jona-Lasinio (NJL) and Polyakov loop extended NJL models (PNJL) which currently are used to extract the thermodynamic characteristics of the quark-gluon system. It is argued that the most attractive resolution of these incongruities is the possibility to obtain the thermodynamic potential directly from the corresponding extremum conditions (gap equations) by integrating them, an integration constant being fixed in accordance with the Stefan-Boltzmann law. The advantage of the approach is that the regulator is kept finite both in divergent and finite valued integrals at finite temperature and chemical potential. The Pauli-Villars regularization is used, although a standard 3D sharp cutoff can be applied as well.Comment: 16 pages, 5 figures, extended version, title change

Finite-Energy Sum Rules in Eta Photoproduction off the Nucleon

The reaction ${\gamma}N \to {\eta}N$ is studied in the high-energy regime (with photon lab energies $E_{\gamma}^{\textrm{lab}} > 4$ GeV) using information from the resonance region through the use of finite-energy sum rules (FESR). We illustrate how analyticity allows one to map the t-dependence of the unknown Regge residue functions. We provide predictions for the energy dependence of the beam asymmetry at high energies.Comment: Joint Physics Analysis Cente

Cryogenic R&D at the CERN Central Cryogenic Laboratory

The Central Cryogenic Laboratory operates since many years at CERN in the framework of cryogenic R&D for accelerators and experiments. The laboratory hosts several experimental posts for small cryogen ic tests, all implemented with pumping facility for GHe and vacuum, and is equipped with a He liquefier producing 6.105 l/year, which is distributed in dewars. Tests include thermomechanical qualifica tion of structural materials, cryogenic and vacuum qualification of prototypes, evaluation of thermal losses of components. Some of the most relevant results obtained at the laboratory in the last yea rs are outlined in this paper

Counting, generating and sampling tree alignments

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis.In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees $S$ and $T$. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal RNA secondary structures alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 201