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

Numerical simulation evidence of dynamical transverse Meissner effect and moving Bose glass phase

We present 3D numerical simulation results of moving vortex lattices in presence of 1D correlated disorder at zero temperature. Our results with field tilting confirm the theoritical predictions of a moving Bose glass phase, characterized by transverse pinning and dynamical transverse Meissner effect, the moving flux lines being localized along the correlated disorder direction. Beyond a critical transverse field, vortex lines exhibit along all their length a "kink" structure resulting from an effective static "tin roof" pinning potential in the transverse direction.Comment: 5 pages, 4 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

MANAGING FULL WAVEFORM LIDAR DATA: A CHALLENGING TASK FOR THE FORTHCOMING YEARS

International audienceThis paper proposes to summarize researches and new advances in full waveform lidar data. After a description of full waveform lidar systems, we will review different methodologies developed to process the waveforms (modelling, correlation, stacking). Applications on urban and vegetated areas are then presented. The paper ends up with recommendations on future research themes

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

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

Terrain surfaces and 3-D landcover classification from small footprint full-waveform lidar data: application to badlands

This article presents the use of new remote sensing data acquired from airborne fullwaveform lidar systems. They are active sensors which record altimeter profiles. This paper introduces a set of methodologies for processing these data. These techniques 5 are then applied to a particular landscape, the badlands, but the methodologies are designed to be applied to any other landscape. Indeed, the knowledge of an accurate topography and a landcover classification is a prior knowledge for any hydrological and erosion model. Badlands tend to be the most significant areas of erosion in the world with the highest erosion rate values. Monitoring and predicting erosion within 10 badland mountainous catchments is highly strategic due to the arising downstream consequences and the need for natural hazard mitigation engineering. Additionaly, beyond the altimeter information, full-waveform lidar data are processed to extract intensity and width of echoes. They are related to the target reflectance and geometry. Wa will investigate the relevancy of using lidar-derived Digital Terrain Models (DTMs) and 15 to investigate the potentiality of the intensity and width information for 3-D landcover classification. Considering the novelty and the complexity of such data, they are presented in details as well as guidelines to process them. DTMs are then validated with field measurements. The morphological validation of DTMs is then performed via the computation of hydrological indexes and photo-interpretation. Finally, a 3-D landcover classification is performed using a Support Vector Machine classifier. The introduction of an ortho-rectified optical image in the classification process as well as full-waveform lidar data for hydrological purposes is then discussed

Thermal Effects in the dynamics of disordered elastic systems

Many seemingly different macroscopic systems (magnets, ferroelectrics, CDW, vortices,..) can be described as generic disordered elastic systems. Understanding their static and dynamics thus poses challenging problems both from the point of view of fundamental physics and of practical applications. Despite important progress many questions remain open. In particular the temperature has drastic effects on the way these systems respond to an external force. We address here the important question of the thermal effect close to depinning, and whether these effects can be understood in the analogy with standard critical phenomena, analogy so useful to understand the zero temperature case. We show that close to the depinning force temperature leads to a rounding of the depinning transition and compute the corresponding exponent. In addition, using a novel algorithm it is possible to study precisely the behavior close to depinning, and to show that the commonly accepted analogy of the depinning with a critical phenomenon does not fully hold, since no divergent lengthscale exists in the steady state properties of the line below the depinning threshold.Comment: Proceedings of the International Workshop on Electronic Crystals, Cargese(2008

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