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Résultats algorithmiques pour le design d’ARN avec contraintes de séquence
No full textNational audienceLe problème du design consiste à concevoir une ou des séquences d’ARN qui vont, dans un modèleénergétique, se replier en une structure cible. Les algorithmes déjà existants dans le domaine negèrent pour la plupart pas l’ajout au problème des contraintes de séquence, c’est-à-dire l’interdictionou l’obligation d’utiliser certains motifs.Zhou et al. (2013) ont proposé un algorithme qui utilise de la génération aléatoire dans un langageformel conditionné par un automate fini qui gère les contraintes de motifs interdits/imposés et unegrammaire non contextuelle qui gère les contraintes imposées par la structure recherchée.On propose ici de se baser sur cet algorithme en y ajoutant des optimisations permettant de réduiresa complexité. Ce travail soulève également des questions ouvertes sur la construction efficace d’unautomate (quasi) minimal, ainsi que l’incorporation de contraintes supplémentaires garantissant lerepliement des séquences engendrées vers une structure cible à l’exclusion de tout autre repliement
Simulation du Comportement sous Irradiation aux Ions Lourds du Nanocomposite Au-SiO2
No full textMetal-glass nanocomposites are interesting owing to their particular optical-properties. Ion irradiation can be used as a tool to fabricate nanocomposites. The aim of this thesis was to study, from a fundamental point of view, the behavior of gold nanoparticles (NPs) embedded in an amorphous silica matrix under irradiation. My contribution consists in the interpretation, by modeling and numerical simulation, of experimental results previously obtained by researchers of the Laboratoire des Solides Irradiés. In a first type of experiments, the system was irradiated with 4 MeV gold ions while in a second type the irradiation was performed by using 74 MeV krypton ions.For the study of the first type of experiments, the simulation by kinetic Monte Carlo (KMC) on rigid lattice was chosen and developed specifically to study the behavior of NPs irradiated at different temperatures. The simulations allows us to reproduce qualitatively the experimental results at any temperature. We found that the system evolves within a direct coarsening regime at high temperature (T>900 K) whereas at low temperatures (T60 nm) by the incident ions. We imagined a scenario for the mechanism of deformation which is based on the thermal expansion of the melted NP into the track produced by the incident ion in the matrix. Its implementation using a new simulation technique helped to refine certain elements of the scenario and to improve the overall understanding of the process. The qualitative agreement between the experimental data and the results obtained by the simulation validate the proposed mechanism.Les matériaux nanocomposites de type métal-verre sont intéressants en raison de leurs propriétés optiques particulières. La technique de fabrication utilisant les faisceaux d’ions est un outil prometteur pour les nanocomposites. L’objectif de cette thèse était d’étudier d’un point de vue fondamental le comportement sous irradiation de nanoparticules (NPs) d’or enfouies dans une matrice de silice amorphe. Ma contribution réside dans l’interprétation par modélisation et simulation numérique des résultats expérimentaux obtenus auparavant par des chercheurs du Laboratoire des Solides Irradiés. Dans le premier type d’expériences, le système a été irradié par des ions d’or de 4 MeV alors que dans le second type l’irradiation est effectuée avec des ions de krypton de 74 MeV.Dans la première partie, la simulation par Monte Carlo cinétique (KMC) sur réseau rigide a été choisie et développée spécifiquement pour étudier le comportement de NPs sous irradiation à différentes températures. Les simulations ont permis de reproduire qualitativement les résultats expérimentaux à toute température. Nous avons retrouvé en particulier le mûrissement d’Ostwald qui se produit à haute température (T>900 K) et la dissolution des NPs qui se produit à basse température (T60 nm) selon l’axe de l’ion incident. Nous avons imaginé un scénario du mécanisme de la déformation qui repose sur la dilatation thermique de la NP métallique fondue dans la région de la trace de l’ion incident. Sa mise en œuvre, grâce à une nouvelle technique de simulation développée spécialement, a permis d’affiner certains éléments du scénario et d’améliorer la compréhension globale du processus. L’accord qualitatif entre les données expérimentales et les résultats obtenus par simulation valide le mécanisme proposé
Systematic study of charged-pion and kaon femtoscopy in Au + Au collisions at √sNN = 200 GeV
No full textInternational audienceWe present a systematic study of charged-pion and kaon interferometry in Au+Au collisions at sNN−−−√=200 GeV. The kaon mean source radii are found to be larger than pion radii in the outward and longitudinal directions for the same transverse mass; this difference increases for more central collisions. The azimuthal-angle dependence of the radii was measured with respect to the second-order event plane and similar oscillations of the source radii were found for pions and kaons. Hydrodynamic models qualitatively describe the similar oscillations of the mean source radii for pions and kaons, but they do not fully describe the transverse-mass dependence of the oscillations
Maximal Lower Bounds in the Loewner order
No full textInternational audienceWe show that the set of maximal lower bounds of two symmetric matrices with respect to Loewner order can be identified to the quotient set O(p,q)/(O(p)×O(q)). Here, (p,q)denotes the inertia of the difference of the two matrices, O(p) is the p-th orthogonal group, and O(p,q) is the indefinite orthogonal group arising from a quadratic form with inertia (p,q). We discuss the application of this result to the synthesis of ellipsoidal invariants of hybrid dynamical systems
Eigenvectors of Non-Linear Maps on the Cone of Positive Semidefinite Matrices Application to Stability Analysis
No full textInternational audienceWe show that the problem of synthesis of a common Lyapunov function for some classes of switched linear systems can be approached by solving an eigenproblem involving a nonlinear map on the cone of positive semidefinite matrices. This map involves the selection of a maximal lower bound of a family of matrices in this cone. We present some variants of the power algorithm, allowing one to solve the nonlinear eigenproblem in a scalable way
Factorization of tropical matrices
No full textInternational audienceIn contrast to the situation in classical linear algebra, not every tropically non-singular matrix can be factored into a product of tropical elementary matrices. We prove the factorizability of any tropically non-singular 2\times 2 matrix, relating to the tropicalization of the existing Bruhat decomposition, and determine which 3\times 3 matrices are factorizable. Nevertheless, there is a closure operation, obtained by means of the tropical adjoint, which is always factorizable, generalizing the decomposition of the tropical closure operation: Kleene star
Late-glacial to late-Holocene shifts in global precipitation δ18O
No full textInternational audienceReconstructions of Quaternary climate are often based on the isotopic content of paleo-precipitation preserved in proxy records. While many paleo-precipitation isotope records are available, few studies have synthesized these dispersed records to explore spatial patterns of late-glacial precipitation δ 18 O. Here we present a synthesis of 86 globally distributed groundwater (n = 59), cave calcite (n = 15) and ice core (n = 12) isotope records spanning the late-glacial (defined as ∼ 50 000 to ∼ 20 000 years ago) to the late-Holocene (within the past ∼ 5000 years). We show that precipitation δ 18 O changes from the late-glacial to the late-Holocene range from −7.1 ‰ (δ 18 O late-Holocene > δ 18 O late-glacial) to +1.7 ‰ (δ 18 O late-glacial > δ 18 O late-Holocene), with the majority (77 %) of records having lower late-glacial δ 18 O than late-Holocene δ 18 O values. High-magnitude, negative precipitation δ 18 O shifts are common at high latitudes, high altitudes and continental interiors (δ 18 O late-Holocene > δ 18 O late-glacial by more than 3 ‰). Conversely, low-magnitude, positive precipitation δ 18 O shifts are concentrated along tropical and subtropical coasts (δ 18 O late-glacial > δ 18 O late-Holocene by less than 2 ‰). Broad, global patterns of late-glacial to late-Holocene precipitation δ 18 O shifts suggest that stronger-than-modern isotopic distillation of air masses prevailed during the late-glacial, likely impacted by larger global temperature differences between the tropics and the poles. Further, to test how well general circulation models reproduce global precipitation δ 18 O shifts, we compiled simulated precipitation δ 18 O shifts from five isotope-enabled general circulation models simulated under recent and last glacial maximum climate states. Climate simulations generally show better inter-model and model-measurement agreement in temperate regions than in the tropics, highlighting a need for further research to better understand how inter-model spread in con-vective rainout, seawater δ 18 O and glacial topography pa-rameterizations impact simulated precipitation δ 18 O. Future research on paleo-precipitation δ 18 O records can use the global maps of measured and simulated late-glacial precipitation isotope compositions to target and prioritize field sites
Enjeux et perspectives des données environnementales massives
No full textInternational audienceCet article présente les enjeux et perspectives des données environnementales massives, et introduit le dossier spécial de la revue Terminal sur le sujet des "big environmental data"
Synchronization in Music Group Playing
No full text- electronic proceedings available at http://cmr.soc.plymouth.ac.uk/cmmr2015/proceedings.pdf-- paper proceedings published by Springer in the LNCS series, in 2016- the article win the best student presentationInternational audienceIn this project, we created an agent-based model of music group playing under four di↵erent interaction mechanisms. Based on real music data, added randomness and simplifying assumptions, we examine how agents synchronize and deviate from the original score. We find that while music can make synchronization complex, it also helps reducing the total deviation. By studying the simulation process, several conclusions on the relationship between di↵erent growing speeds of total deviations and di↵erent interaction schemes are drawn. With interpretation from a musical point of view, we find that, in a music ensemble, listening to neighbors helps the players end up in sync. However, if people do not listen carefully enough, the deviation becomes larger than when people do not listen at all. On the issue of whom one should listen to, the results show no significant di↵erences between listening to the immediate neighbors and to the whole group. Finally, we also observe that large deviations can be reduced by making the musicians move while playing