Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The influence of redox alteration on the growth and proteomic pattern of Listeria monocytogenes was investigated. A redox shock was induced in cultures by addition of 3mM ferricyanide (FeCN) and 6mM dithiothreitol (DTT) to increase or to decrease respectively the redox potential naturally occurring at the beginning of growth. In both conditions, the reducing and oxidizing redox shock had a strong influence, decreasing the maximum growth rate by half compared to a control culture. The proteomic analysis of L. monocytogenes performed by two-dimensional difference gel electrophoresis (2D-DIGE) exhibited twenty-three proteins differentially expressed (P<0.05), among these, many were oxidoreductases, and proteins involved in cellular metabolism (glycolysis, protein synthesis), detoxification (kat) or adhesion (Lmo1634).
ISSN: 1874-3919

hal-00877138
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00877138
DOI : 10.1016/j.jprot.2012.11.010
PUBMED : 23195917

Éditeur(s) : Amer Meteorological Soc
Résumé : The Congo River has the second largest rate of flow in the world and is mainly responsible for the broad tongue of low-salinity water that is observed in the Gulf of Guinea. Despite their importance, near-equatorial river plumes have not been studied as thoroughly as midlatitude plumes and their dynamics remain unclear. Using both theory and idealized numerical experiments that reproduce the major characteristics of the region, the authors have investigated the dynamics of the Congo River plume and examine its sensitivity to different forcing mechanisms. It is found that near-equatorial plumes are more likely to be surface trapped than midlatitude plumes, and the importance of the effect in describing the strong offshore extent of the low-salinity tongue during most of the year is demonstrated. It is shown that the buoyant plume constrained by the geomorphology is subject to the pulling of nonlinear structures and wavelike equatorial dynamics. The wind is found to strengthen the intrinsic buoyancy-driven dynamics and impede the development of the coastal southward current, in coherence with observations.
Journal Of Physical Oceanography (0022-3670) (Amer Meteorological Soc), 2014-03 , Vol. 44 , N. 3 , P. 980-994

Droits : 2014 American Meteorological Society
http://archimer.ifremer.fr/doc/00187/29850/28298.pdf
DOI:10.1175/JPO-D-13-0132.1
http://archimer.ifremer.fr/doc/00187/29850/

Éditeur(s) : HAL CCSD
Résumé : International audience
We consider a second-order differential system with Hessian-driven damping . An interesting property of this system is that, after introduction of an auxiliary variable y , it can be equivalently written as a first-order system in time and space. This allows us to extend the analysis to the case of a convex lower semicontinuous potential and so to introduce constraints in the model. When considering the indicator function of a closed convex set, the subdifferential operator takes account of the contact forces. In this setting, by playing with the geometrical damping parameter, we can describe nonelastic shock laws with restitution coefficient. Taking advantage of the infinite dimensional framework, we introduce a nonlinear hyperbolic PDE describing a damped oscillating system with obstacle. The system is dissipative; in the convex case each trajectory weakly converges to a minimizer of the global potential energy function. Exponential stabilization is obtained under strong convexity assumptions.
Differential Equations & Applications

hal-00803214
https://hal.archives-ouvertes.fr/hal-00803214
https://hal.archives-ouvertes.fr/hal-00803214/document
https://hal.archives-ouvertes.fr/hal-00803214/file/Attouch-Mainge-Redont-30August2011.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The full numerical simulation of turbulent flows in the context of industrial applications remains a very challenging problem. One of the difficulties is the presence of a large number of interacting scales of different orders of magnitude, ranging from the macroscopic scale to the Kolmogorov dissipation scale. In order to better understand and simulate these interactions, new algorithms of incremental type have recently been introduced, stemming from the theory of infinite-dimensional dynamical systems (see, e.g., the algorithms of Foias, Jolly et al. (1988), Foias, Manley and Temam (1988), Laminie et al. (1993, 1994), Marion and Temam (1989, 1990), and Temam (1990)). These algorithms are based on decompositions of the unknown functions into a large- and a small-scale component, one of the underlying ideas being to approximate the corresponding attractor. In the context of finite element methods, the decomposition of a solution into small- and large-scale components appears when we consider hierarchical bases (Yserentant, 1986; Zienkiewicz et al., 1982). In the present article we derive several estimates of the size of the structures for the linear and nonlinear terms which correspond to interactions of different hierarchical components of the velocity field, and also their time variation. The one-step time variation of these terms can be smaller than the expected accuracy of the computation. Using this remark, we implement an adaptive spatial and temporal multilevel algorithm which treats differently the small- and large-scale components of the flow. We derive several a priori estimates in order to study the perturbation introduced into the approximated equations. All the interaction terms between small- and large-scale structures are frozen during several time steps. Finally, we implement the multilevel method in order to simulate a bidimensional flow described by the Burgers equations. We perform a parametric study of the procedure and its efficiency. The gain in CPU time is significant and the trajectories computed by our multi-scale method remain close to the trajectories obtained with the classical Galerkin method.
ISSN: 0168-9274

hal-00730710
https://hal.archives-ouvertes.fr/hal-00730710

Éditeur(s) : HAL CCSD Intech
Résumé : International audience
The massive integration of sustainable energies into electrical grids (non-interconnectedor connected) is a major problem due to their stochastic character revealed by strongfluctuations at all scales. In this paper, the scaling behaviour or power law correlationsand the nature of scaling behaviour of sustainable resource data such as flow velocity,atmospheric wind speed, solar global solar radiation and sustainable energy such as,wind power output, are highlighted. For the first time, Fourier power spectral densitiesare estimated for each dataset. We show that the power spectrum densities obtained areclose to the 5/3 Kolmogorov spectrum. Furthermore, the multifractal and intermittentproperties of sustainable resource and energy data have been revealed by the concavityof the scaling exponent function. The proposed analysis frame allows a full descriptionof fluctuations of processes considered. A good knowledge of the dynamic of fluctua-tions is crucial to management of the integration of sustainable energies into a grid.
Sustainable Energy - Technological Issues, Applications and Case Studies

hal-01528087
https://hal.archives-ouvertes.fr/hal-01528087
DOI : 10.5772/106341

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Algorithms issued from the NonLinear Galerkin method have been used in many situations and with different discretizations for the resolution of evolutionary nonlinear equations. The main idea of these methods is to use a splitting of the solution in order to model the equation. According to the splitting of the solution, a splitting of the equation is obtained. The modeling principle is to freeze terms which have a small time variation. In this work we use wavelet discretizations of the 2-D Burgers equations and compare the results with the hierarchical finite elements method. The numerical tests indicate that wavelets give better results than finite elements
ISSN: 0885-7474

hal-00383423
https://hal.archives-ouvertes.fr/hal-00383423
DOI : 10.1007/s10915-004-4806-4

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper is concerned with a null controllability problem for nonlinear parabolic equations appearing in mathematical biology. We consider a system of two equations with a nonlocal nonlinearity, in a bounded domain Ω of ℝN0, N0 being a positive integer sufficiently small. Such models can be used in the context of dynamics of biological systems to describe the migration of population (of bacteria in a container). Our aim is to find a control common to both equations, which solves the null controllabillity of the studied system under constraints on the state. A similar control problem has recently been addressed for the Laplace operator, so the present paper extends those results.
2017 Proceedings of the Conference on Control and its Applications
Pittsburgh, United States

Droits : http://hal.archives-ouvertes.fr/licences/copyright/
hal-01567339
https://hal.archives-ouvertes.fr/hal-01567339
DOI : 10.1137/1.9781611975024.3

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Coral reefs are increasingly being altered by a myriad of anthropogenic activities and natural disturbances. Long-term studies offer unique opportunities to understand how multiple and recurrent disturbances can influence coral reef resilience and long-term dynamics. While the long-term dynamics of coral assemblages have been extensively documented, the long-term dynamics of coral reef fish assemblages have received less attention. Here, we describe the changes in fish assemblages on Tiahura reef, Moorea, from 1979 to 2011. During this 33-yr period, Tiahura was exposed to multiple disturbances (crown-of-thorns seastar outbreaks and cyclones) that caused recurrent declines and recoveries of coral cover and changes in the dominant coral genera. These shifts in coral composition were associated with long-term cascading effects on fish assemblages. The composition and trophic structure of fish assemblages continuously shifted without returning to their initial composition, whereas fish species richness remained stable, albeit with a small increase over time. We detected nonlinear responses of fish density when corals were most degraded. When coral cover dropped below 10 % following a severe crown-of-thorns sea star outbreak, the density of most fish trophic groups sharply decreased. Our study shows that historical contingency may potentially be an important but largely underestimated factor explaining the contemporary structure of reef fish assemblages and suggests that temporal stability in their structure and function should not necessarily be the target of management strategies that aim at increasing or maintaining coral reef resilience.
ISSN: 0722-4028

hal-01282725
https://hal-univ-perp.archives-ouvertes.fr/hal-01282725
DOI : 10.1007/s00338-015-1371-2

Résumé : Cette thèse à pour objet l'étude théorique et numérique de solutions dans les équations aux dérivées partielles non linéaires de la physique, en particulier en dynamique des fluides. La présence de discontinuités dans les solutions de ces équations complique la compréhension mathématique des phénomènes mis enjeu et leur traitement numérique, notamment en vue de simulations informatiques . Nous étudions ces équations par une méthode de régularisation dans un espace fonctionnel approprié. Lorsque des schémas numériques construits par des méthodes différentes conduisent à des résultats identiques, ceci jusque dans leurs moindres détails, il semble alors naturel de s'interroger dans quelle mesure ces suites de solutions numériques constituent une approximation d'une solution des équations étudiées. Nous construisons des suites de solutions approchées à partir d'un schéma numérique original,stable et suffisamment simple pour démontrer que ses suites constituent une méthode asymptotique de Maslov au sens des distributions en dimension trois d'espèce. La technique de régularisation employée consiste à étendre les variables réelles du problème ne des variables complexes, ce qui nous permet de construire des familles de solutions particulières que l'on ramène au cas réel en faisant tendre un petit paramètre vers O. Les solutions physiques recherchées apparaissent alors comme valeurs au bord de fonction holomorphes. Nous illustrons les résultats obtenus par des applications en cosmologie dans les cadres Newtoniens et relativistes pour des systèmes sans pression, puis avec pression et auto-gravitation, ainsi que pour le système des gaz parfaits.
This thesis is devoted to the theoretical and numerical study of singular solutions appearing in nonlinear partial differential complicates the mathematical understanding of the phenomena under concem as well as their numerical treatment, in particular in view of computation. These equations are studied by a regularization method in an appropriate functional space. When completely different numerical methods give the same results up to the smallest details one can reasonably expect that these numerical results suggest the existence of a mathematical solution of theses equations. We construct sequences of approximate solutions from an original numerical scheme, which is stable and simple enough to prove that these sequences constitute a Maslov asymptotic method in three space dimension. The regularization technique in use consits in extending the real variables of the problem into complex ones, which perrnits to construct families of particular equations that we bring back to the real case by letting a small paramater tend to zero. The expected physical solutions appear as boundary values of holomorphie functions . Illustrations are given by applications to cosmology in the Newtorian and re1ativistic settings for pressure1ess fluid dynamics, then in presence of self-gravitation and pressure as weil as for the systemof ideal gases

http://www.theses.fr/2011AGUY0478/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The quasi-equilibrium approximation is acceptable when molecular interactions are fast enough compared to circuit dynamics, but is no longer allowed when cellular activities are governed by rare events. A typical example is the lactose operon (lac), one of the most famous paradigms of transcription regulation, for which several theories still coexist to describe its behaviors. The lac system is generally analyzed by using equilibrium constants, contradicting single-event hypotheses long suggested by Novick and Weiner (1957). Enzyme induction as an all-or-none phenomenon. Proc. Natl. Acad. Sci. USA 43, 553-566) and recently refined in the study of (Choi et al., 2008. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322, 442-446). In the present report, a lac repressor (LacI)-mediated DNA immunoprecipitation experiment reveals that the natural LacI-lac DNA complex built in vivo is extremely tight and long-lived compared to the time scale of lac expression dynamics, which could functionally disconnect the abortive expression bursts and forbid using the standard modes of lac bistability. As alternatives, purely kinetic mechanisms are examined for their capacity to restrict induction through: (i) widely scattered derepression related to the arrival time variance of a predominantly backward asymmetric random walk and (ii) an induction threshold arising in a single window of derepression without recourse to nonlinear multimeric binding and Hill functions. Considering the complete disengagement of the lac repressor from the lac promoter as the probabilistic consequence of a transient stepwise mechanism, is sufficient to explain the sigmoidal lac responses as functions of time and of inducer concentration. This sigmoidal shape can be misleadingly interpreted as a phenomenon of equilibrium cooperativity classically used to explain bistability, but which has been reported to be weak in this system.
ISSN: 0022-5193

inserm-00818506
http://www.hal.inserm.fr/inserm-00818506
http://www.hal.inserm.fr/inserm-00818506/document
http://www.hal.inserm.fr/inserm-00818506/file/LacI-TeX.pdf
ARXIV : 1312.5566

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
A hallmark of living systems is the management and the storage of information through genetic and epigenetic mechanisms. Although the notion of epigenetics was originally given to any regulation beyond DNA sequence, it has often been restricted to chromatin modifications, supposed to behave as cis-markers, specifying the sets of genes to be expressed or repressed. This definition does not take into account the initial view of epigenetics, based on nonlinear interaction networks whose "attractors" can remain stable without need for any chromatin mark. In addition, most chromatin modifications are the steady state resultants of highly dynamic modification and de-modification activities and, as such, seem poorly appropriate to work as long-term memory keepers. Instead, the basic support of epigenetic memory could remain the attractors, to which chromatin modifications belong as do many other components. The influence of chromatin modifications in memory is highly questionable when envisioned as static structural marks, but can be recovered under the dynamic circuitry perspective, thanks to their self-templating properties. Beside their standard repressive or permissive functions, chromatin modifications can also influence transcription in multiple ways such as: (1) by randomizing or inversely stabilizing gene expression, (2) by mediating cooperativity between pioneer and secondary transcription factors, and (3) in the hysteresis and the ultrasensitivity of gene expression switches, allowing the cells to take unambiguous transcriptional decisions.
ISSN: 1420-682X

hal-01063617
https://hal.archives-ouvertes.fr/hal-01063617
DOI : 10.1007/s00018-012-0923-7
PUBMED : 22331281

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The objectives are to study and model the aggregate wind power fluctuations dynamics in the multifractal framework. We present here the analysis of aggregate power output sampled at 1 Hz during three years. We decompose the data into several Intrinsic Mode Functions (IMF) using Empirical Mode Decomposition (EMD). We use a new approach, arbitrary order Hilbert spectral analysis, a combination of EMD approach with Hilbert spectral analysis (or Hilbert Huang Transform) and the classical structure function analysis to extract the scaling exponents or multifractal spectrum $zeta(q)$: this function provides a full characterization of a process at all intensities and all scales. The application of both methods, i.e. structure function and arbitrary-order Hilbert spectral analyses, give similar results indicating that the aggregate power output from a wind farm, possesses intermittent and multifractal properties. In order to check this result, we generate stochastic simulations of a Multifractal Random Walk (MRW) using a log-normal stochastic equation. We show that the simulation results are fully compatible with the experimental results.
Physica A

hal-01527887
https://hal.archives-ouvertes.fr/hal-01527887
DOI : 10.1016/j.physa.2013.04.038

Éditeur(s) : HAL CCSD
Résumé : International audience
The present work concerns cuspate spits: slightly symmetrical geomorphic features growing along the shoreline in shallow waters. We develop a new formulation for the dynamics of cuspate spits. Our approach relies on classical paradigms such as a conservation law to the shoreface scale and an explicit formula for alongshore sediment transport. We derive a non-linear diffusion equation and a fully explicit solution for the growth of cuspate spits. From this general expression, we found interesting applications to quantify shoreline dynamics in the presence of cuspate spits. In particular, we point out a simple method for the datation of a cuspate spit given a limited number of input parameters. Furthermore, we develop a method to quantify the mean alongshore diffusivity along a shoreline perturbed by well-defined cuspate spits of known sizes. Finally, we introduce a formal relationship between the geometric characteristics (amplitude, length) of cuspate spits, which reproduce the self-similarity of these geomorphic features.
13th International Coastal Symposium
Durban, South Africa

hal-01006569
https://hal.archives-ouvertes.fr/hal-01006569
https://hal.archives-ouvertes.fr/hal-01006569/document
https://hal.archives-ouvertes.fr/hal-01006569/file/JCR_SI_70_009_Bouchette_et_al.pdf