1,372 research outputs found
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 and the arc-preserving subsequence problem is to
determine if can be obtained from by deleting bases from . 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 time
and space, where and are the lengths of and , respectively. In
this paper we present a new algorithm using time and 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 and 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 is studied in the high-energy regime
(with photon lab energies 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
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 and . 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
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
- âŠ