FFT-based algorithms for the string matching with mismatches problem

The string matching with mismatches problem requires finding the Hamming distance between a pattern P of length m and every length m substring of text T with length n. Fischer and Paterson's FFT-based algorithm solves the problem without error in O(σnlogm), where σ is the size of the alphabet Σ [SIAM–AMS Proc. 7 (1973) 113–125]. However, this in the worst case reduces to O(nmlogm). Atallah, Chyzak and Dumas used the idea of randomly mapping the letters of the alphabet to complex roots of unity to estimate the score vector in time O(nlogm) [Algorithmica 29 (2001) 468–486]. We show that the algorithm's score variance can be substantially lowered by using a bijective mapping, and specifically to zero in the case of binary and ternary alphabets. This result is extended via alphabet remappings to deterministically solve the string matching with mismatches problem with a constant factor of 2 improvement over Fischer–Paterson's method.     

Practical algorithms for transposition-invariant string-matching

We consider the problems of (1) longest common subsequence (LCS) of two given strings in the case where the first may be shifted by some constant (that is, transposed) to match the second, and (2) transposition-invariant text searching using indel distance. These problems have applications in music comparison and retrieval. We introduce two novel techniques to solve these problems efficiently. The first is based on the branch and bound method, the second on bit-parallelism. Our branch and bound algorithm computes the longest common transposition-invariant subsequence (LCTS) in time O((m²+loglogσ)logσ) in the best case and O((m²+logσ)σ) in the worst case, where m and σ, respectively, are the length of the strings and the size of the alphabet. On the other hand, we show that the same problem can be solved by using bit-parallelism and thus obtain a speedup of O(w/logm) over the classical algorithms, where the computer word has w bits. The advantage of this latter algorithm over the present bit-parallel ones is that it allows the use of more complex distances, including general integer weights. Since our branch and bound method is very flexible, it can be further improved by combining it with other efficient algorithms such as our novel bit-parallel algorithm. We experiment on several combination possibilities and discuss which are the best settings for each of those combinations. Our algorithms are easily extended to other musically relevant cases, such as δ-matching and polyphony (where there are several parallel texts to be considered). We also show how our bit-parallel algorithm is adapted to text searching and illustrate its effectiveness in complex cases where the only known competing method is the use of brute force.     

De Sitter universes and the emerging landscape in string theory

We discuss a recent proposal to construct de Sitter vacua in string theory. It is based on flux compactifications in string theory where all the moduli are stabilised and supersymmetry is broken with control. The resulting picture is that of a complicated landscape with many vacua of widely varying values for the cosmological constant.     

Vibration of strings with nonlinear supports

The dynamic string motion, which displacement is unilaterally constrained by the rigid termination condition of an arbitrary geometry has been simulated and analyzed. The treble strings of a grand piano usually terminate at a capo bar, which is situated above the strings. The apex of a V-shaped section of the capo bar defines the end of the speaking length of the strings. A numerical calculation based on the traveling wave solution is proposed for modeling the nonlinearity inducing interactions between the vibrating string and the contact condition at the point of string termination. It was shown that the lossless string vibrates in two distinct vibration regimes. In the beginning the string starts to interact in a nonlinear fashion with the rigid terminator, and the resulting string motion is aperiodic. Consequently, the spectrum of the string motion depends on the amplitude of string vibrations, and its spectral structure changes continuously with the passage of time. The duration of that vibration regime depends on the geometry of the terminator. After some time of aperiodic vibration, the string vibrations settle in a periodic regime where the resulting spectrum remains constant.     

Variations on the warped deformed conifold

The warped deformed conifold background of type IIB theory is dual to the cascading SU(M(p+1))×SU(Mp) gauge theory. We show that this background realizes the (super-)Goldstone mechanism where the U(1) baryon number symmetry is broken by expectation values of baryonic operators. The resulting massless pseudo-scalar and scalar glueballs are identified in the supergravity spectrum. A D-string is then dual to a global string in the gauge theory. Upon compactification, the Goldstone mechanism turns into the Higgs mechanism, and the global strings turn into ANO strings. To cite this article: S.S. Gubser et al., C. R. Physique 5 (2004).

Résumé

La configuration de fond pour la théorie de type IIB donnée par le conifold voilé déformé est duale à la cascade de théorie de jauge SU(M(p+1))×SU(Mp). Nous montrons que cette configuration donne une réalisation du mécanisme de (super-)Goldstone où la symètrie baryonique U(1) est brisée par la valeur moyenne dans le vide des opérateurs baryoniques. Les boules de glue pseudo-scalaires et scalaires de masse nulle résultantes sont identifiées dans le spectre de supegravité. Une D-corde est alors duale à une corde globale dans la théorie de jauge. Après compactification, le mécanisme de Goldstone devient un mécanisme de Higgs, et une corde globale devient une corde ANO. Pour citer cet article : S.S. Gubser et al., C. R. Physique 5 (2004).     

Higher spin gauge theories in any dimension

Some general properties of higher spin gauge theories are summarized, with the emphasize on the nonlinear theories in any dimension. To cite this article: M.A. Vasiliev, C. R. Physique 5 (2004).

Résumé

Des propriétés générales des théories de jauge de grands spins sont présentées, en insistant particulièrement sur les théories non-linéaires en dimensions diverses. Pour citer cet article : M.A. Vasiliev, C. R. Physique 5 (2004).     

Are Axidilaton Stars Massive Compact Halo Objects?

Boson stars built from a very light Kalb–Ramond axion, the dilaton or other moduli fields of effective string models could provide a considerable fraction of the non-baryonic part of dark matter. Gravitational microlensing of 0.5 M MACHOs within the halo of galaxies may indirectly "weighing" the mass of the constituent scalar particle, resulting in 10^–10 eV/c².     

Strategies of loop recombination in ciliates

The concept of breakpoint graph, known from the theory of sorting by reversal, has been successfully applied in the theory of gene assembly in ciliates. We further investigate its usage for gene assembly, and show that the graph allows for an efficient characterization of the possible orders of loop recombination operations (one of the three types of molecular operations that accomplish gene assembly) for a given gene during gene assembly. The characterization is based on spanning trees within a graph built upon the connected components in the breakpoint graph. We work in the abstract and more general setting of so-called legal strings.     

A Lagrangian representation of tangles

We construct a functor from the category of oriented tangles in R³ to the category of Hermitian modules and Lagrangian relations over Z[t,t^-1]. This functor extends the Burau representations of the braid groups and its generalization to string links due to Le Dimet.