Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction

A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has the C1P. Such submatrices have been considered in comparative genomics applications, but very little is known about their combinatorial structure and efficient algorithms to compute them. We first describe an algorithm that detects rows that belong to Minimal Conflicting Sets. This algorithm has a polynomial time complexity when the number of 1's in each row of the considered matrix is bounded by a constant. Next, we show that the problem of computing all Minimal Conflicting Sets can be reduced to the joint generation of all minimal true clauses and maximal false clauses for some monotone boolean function. We use these methods on simulated data related to ancestral genome reconstruction to show that computing Minimal Conflicting Set is useful in discriminating between true positive and false positive ancestral syntenies. We also study a dataset of yeast genomes and address the reliability of an ancestral genome proposal of the Saccahromycetaceae yeasts.Comment: 20 pages, 3 figure

Creep via dynamical functional renormalization group

We study a D-dimensional interface driven in a disordered medium. We derive finite temperature and velocity functional renormalization group (FRG) equations, valid in a 4-D expansion. These equations allow in principle for a complete study of the the velocity versus applied force characteristics. We focus here on the creep regime at finite temperature and small velocity. We show how our FRG approach gives the form of the v-f characteristics in this regime, and in particular the creep exponent, obtained previously only through phenomenological scaling arguments.Comment: 4 pages, 3 figures, RevTe

Effects of wall compliance on the laminar–turbulent transition of torsional Couette flow

Torsional Couette flow between a rotating disk and a stationary wall is studied experimentally. The surface of the disk is either rigid or covered with a compliant coating. The influence of wall compliance on characteristic flow instabilities and on the laminar–turbulent flow transition is investigated. Data obtained from analysing flow visualizations are discussed. It is found that wall compliance favours two of the three characteristic wave patterns associated with the transition process and broadens the parameter regime in which these patterns are observed. The results for the effects of wall compliance on the third pattern are inconclusive. However, the experiments indicate that the third pattern is not a primary constituent of the laminar–turbulent transition process of torsional Couette flow

Drift of a polymer chain in disordered media

We consider the drift of a polymer chain in a disordered medium, which is caused by a constant force applied to the one end of the polymer, under neglecting the thermal fluctuations. In the lowest order of the perturbation theory we have computed the transversal fluctuations of the centre of mass of the polymer, the transversal and the longitudinal size of the polymer, and the average velocity of the polymer. The corrections to the quantities under consideration, which are due to the interplay between the motion and the quenched forces, are controlled by the driving force and the degree of polymerization. The transversal fluctuations of the Brownian particle and of the centre of mass of the polymer are obtained to be diffusive. The transversal fluctuations studied in the present Letter may also be of relevance for the related problem of the drift of a directed polymer in disordered media and its applications.Comment: 11 pages, RevTex, Accepted for publication in Europhysics Letter

PRINCE: Accurate approximation of the copy number of tandem repeats

Variable-Number Tandem Repeats (VNTR) are genomic regions where a short sequence of DNA is repeated with no space in between repeats. While a fixed set of VNTRs is typically identified for a given species, the copy number at each VNTR varies between individuals within a species. Although VNTRs are found in both prokaryotic and eukaryotic genomes, the methodology called multi-locus VNTR analysis (MLVA) is widely used to distinguish different strains of bacteria, as well as cluster strains that might be epidemiologically related and investigate evolutionary rates. We propose PRINCE (Processing Reads to Infer the Number of Copies via Estimation), an algorithm that is able to accurately estimate the copy number of a VNTR given the sequence of a single repeat unit and a set of short reads from a whole-genome sequence (WGS) experiment. This is a challenging problem, especially in the cases when the repeat region is longer than the expected read length. Our proposed method computes a statistical approximation of the local coverage inside the repeat region. This approximation is then mapped to the copy number using a linear function whose parameters are fitted to simulated data. We test PRINCE on the genomes of three datasets of Mycobacterium tuberculosis strains and show that it is more than twice as accurate as a previous method. An implementation of PRINCE in the Python language is freely available at https://github.com/WGS-TB/PythonPRINCE

The depinning transition of a driven interface in the random-field Ising model around the upper critical dimension

We investigate the depinning transition for driven interfaces in the random-field Ising model for various dimensions. We consider the order parameter as a function of the control parameter (driving field) and examine the effect of thermal fluctuations. Although thermal fluctuations drive the system away from criticality the order parameter obeys a certain scaling law for sufficiently low temperatures and the corresponding exponents are determined. Our results suggest that the so-called upper critical dimension of the depinning transition is five and that the systems belongs to the universality class of the quenched Edward-Wilkinson equation.Comment: accepted for publication in Phys. Rev.

Functional renormalization group at large N for random manifolds

We introduce a method, based on an exact calculation of the effective action at large N, to bridge the gap between mean field theory and renormalization in complex systems. We apply it to a d-dimensional manifold in a random potential for large embedding space dimension N. This yields a functional renormalization group equation valid for any d, which contains both the O(epsilon=4-d) results of Balents-Fisher and some of the non-trivial results of the Mezard-Parisi solution thus shedding light on both. Corrections are computed at order O(1/N). Applications to the problems of KPZ, random field and mode coupling in glasses are mentioned

«Paramphistomum daubneyi » Dinnik 1962

Un trématode encore inconnu en France, Paramphistomum daubneyi Dinnik, 1962, a été recueilli dans les réservoirs gastriques de bovins originaires du Maine-et-Loire et du nord du département de la Loire. Comme Fasciola hepática, ce parasite évolue par l'intermédiaire de Lymnaea truncatula. L’une des espèces les plus voisines, Paramphistomum microbothrium Fischœder, 1901, semble n’exister qu’en Corse, à l’exclusion de toute la France continentale. Le rôle pathogène de Paramphistomum daubneyi est discuté.The authors point out, for the first time, the presence of Paramphistomum daubneyi Dinnik, 1962 in the rumen of cattle originating from Loire and Maine- et-Loire departments (France). As Fasciola hepática, the intermediate host is a lymnaeid snail, Lymnaea truncatula. It seems that the very closely related species Paramphistomum microbo thrium Fischœder, 1901 which develops exclusively in Bulinid snails occurs only in Corsica to the exclusion of french continental territory where Bulinids are not indigeneous. The pathological action of Paramphistomum daubneyi is discussed

Functional Renormalization Group and the Field Theory of Disordered Elastic Systems

We study elastic systems such as interfaces or lattices, pinned by quenched disorder. To escape triviality as a result of ``dimensional reduction'', we use the functional renormalization group. Difficulties arise in the calculation of the renormalization group functions beyond 1-loop order. Even worse, observables such as the 2-point correlation function exhibit the same problem already at 1-loop order. These difficulties are due to the non-analyticity of the renormalized disorder correlator at zero temperature, which is inherent to the physics beyond the Larkin length, characterized by many metastable states. As a result, 2-loop diagrams, which involve derivatives of the disorder correlator at the non-analytic point, are naively "ambiguous''. We examine several routes out of this dilemma, which lead to a unique renormalizable field-theory at 2-loop order. It is also the only theory consistent with the potentiality of the problem. The beta-function differs from previous work and the one at depinning by novel "anomalous terms''. For interfaces and random bond disorder we find a roughness exponent zeta = 0.20829804 epsilon + 0.006858 epsilon^2, epsilon = 4-d. For random field disorder we find zeta = epsilon/3 and compute universal amplitudes to order epsilon^2. For periodic systems we evaluate the universal amplitude of the 2-point function. We also clarify the dependence of universal amplitudes on the boundary conditions at large scale. All predictions are in good agreement with numerical and exact results, and an improvement over one loop. Finally we calculate higher correlation functions, which turn out to be equivalent to those at depinning to leading order in epsilon.Comment: 42 pages, 41 figure

2-loop Functional Renormalization Group Theory of the Depinning Transition

We construct the field theory which describes the universal properties of the quasi-static isotropic depinning transition for interfaces and elastic periodic systems at zero temperature, taking properly into account the non-analytic form of the dynamical action. This cures the inability of the 1-loop flow-equations to distinguish between statics and quasi-static depinning, and thus to account for the irreversibility of the latter. We prove two-loop renormalizability, obtain the 2-loop beta-function and show the generation of "irreversible" anomalous terms, originating from the non-analytic nature of the theory, which cause the statics and driven dynamics to differ at 2-loop order. We obtain the roughness exponent zeta and dynamical exponent z to order epsilon^2. This allows to test several previous conjectures made on the basis of the 1-loop result. First it demonstrates that random-field disorder does indeed attract all disorder of shorter range. It also shows that the conjecture zeta=epsilon/3 is incorrect, and allows to compute the violations, as zeta=epsilon/3 (1 + 0.14331 epsilon), epsilon=4-d. This solves a longstanding discrepancy with simulations. For long-range elasticity it yields zeta=epsilon/3 (1 + 0.39735 epsilon), epsilon=2-d (vs. the standard prediction zeta=1/3 for d=1), in reasonable agreement with the most recent simulations. The high value of zeta approximately 0.5 found in experiments both on the contact line depinning of liquid Helium and on slow crack fronts is discussed.Comment: 32 pages, 17 figures, revtex