Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Numerical programs for simulating flow and reactive transport in porous media is essential for predicting reservoir properties related to CO2 sequestration performance, subsurface storage and risk assessment. In this paper we solve the Navier Stokes' equation using finite difference method, on a simulated porous rock structure, to study the velocity distribution of fluid flowing through it under a constant pressure gradient. A reactive solute carried through the fluid is allowed to interact with the minerals in the rock. This chemical reaction dissolves the mineral which changes the rock structure thus affecting its flow properties. These changes of flow properties are studied with variation in reactive solute concentration and pressure field. The different mechanisms of dissolution responsible for the variation of flow properties for the different parameters is predicted. Before the onset of homogeneous dissolution, variation in porosity follows a power-law behaviour with change in permeability when the latter is scaled by the concentration of the reactive species. The simulation results are compared with available experimental data and found to give a reasonable match.
ISSN: 0022-1694

hal-00757760
https://hal.archives-ouvertes.fr/hal-00757760
DOI : 10.1016/j.jhydrol.2012.05.024

Éditeur(s) : HAL CCSD Humana Press
Résumé : International audience
The sodium-proton exchanger 1 (NHE-1) is a membrane transporter that exchanges Na(+) for H(+) ion across the membrane of eukaryotic cells. It is cooperatively activated by intracellular protons, and this allosteric regulation is modulated by the biophysical properties of the plasma membrane and related lipid environment. Consequently, NHE-1 is a mechanosensitive transporter that responds to osmotic pressure, and changes in membrane composition. The purpose of this study was to develop the relationship between membrane surface tension, and the allosteric balance of a mechanosensitive transporter such as NHE-1. In eukaryotes, the asymmetric composition of membrane leaflets results in a difference in surface tensions that is involved in the creation of a reservoir of intracellular vesicles and membrane buds contributing to buffer mechanical constraints. Therefore, we took this phenomenon into account in this study and developed a set of relations between the mean surface tension, membrane asymmetry, fluid phase endocytosis and the allosteric equilibrium constant of the transporter. We then used the experimental data published on the effects of osmotic pressure and membrane modification on the NHE-1 allosteric constant to fit these equations. We show here that NHE-1 mechanosensitivity is more based on its high sensitivity towards the asymmetry between the bilayer leaflets compared to mean global membrane tension. This compliance to membrane asymmetry is physiologically relevant as with their slower transport rates than ion channels, transporters cannot respond as high pressure-high conductance fast-gating emergency valves.
ISSN: 1085-9195

inserm-00871709
http://www.hal.inserm.fr/inserm-00871709
http://www.hal.inserm.fr/inserm-00871709/document
http://www.hal.inserm.fr/inserm-00871709/file/art_3A10.1007_2Fs12013-012-9340-7.pdf
DOI : 10.1007/s12013-012-9340-7

Éditeur(s) : HAL CCSD
Résumé : International audience
In the paper the following mixed equilibrium problem in a Hilbert space is considered: find x 2 C such that F(x, x)+hG(x), x−xi 0, 8x 2 C, where C is a nonempty convex closed subset of a real Hilbert space. For its solution a version of the proximal approach is studied. The general proximal method always includes a quadratic term of the kind |x−xn|2, which provides a process of transition from a point xn to a point xn+1. The authors replace this quadratic term by its linearization. Thus, they obtain a method of the kind F(xn+1, x)+hG(xn)+ −1(h 0(xn+1)−h 0(xk)), x−xn+1i 0, 8x 2 C, where h0 is the derivative of a given function on C. It is proved that if the function F(x, y) is monotone and convex in y for any x, F(x, x) = 0, and the operator G(x) is co-coercive, then the method weakly converges in a real Hilbert space to an equilibrium solution. Note that this result will also be true if the co-coercive condition is replaced by a monotonicity property. The Tikhonov regularization method (in the absence of disturbances and calculating auxiliary solutions approximately) is justified and its weak convergence in a Hilbert space is proved. It is known that the proximal method can always be interpreted as an implicit discret approximation of some differential equation or inclusion. Therefore the authors consider a differential inclusion for the extreme mapping. Permitting "-approximation for the function F(x, y) by means of a parametric family F(x, y, ") and assuming the strong monotonicity of the operator @F(x, y, ") (it is a very strong condition), the authors prove the convergence of the trajectory of the differential inclusion to an equilibrium solution.
Ill-posed variational problems and regularization techniques

hal-00773204
https://hal.univ-antilles.fr/hal-00773204

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Analog sandbox models have been set up to study the impact of syntectonic erosion on thrust wedges with one and two decollement levels. Different accretion mechanisms are activated depending on interactions between surface processes and wedge mechanics: frontal accretion, backthrusting, underthrusting and underplating due to decollement induced duplex formation at depth. These mechanisms may function simultaneously, being located at different parts across the wedge. For all the experiments, a high friction is imposed at the base of models and the volume of eroded material remains equal to the volume of newly accreted material, maintaining a constant surface slope during the shortening. Erosion limits the forward propagation of thrust wedges and favors the underthrusting of basal layers allowing duplex formation. Erosion promotes development of major backthrusts in the thrust wedges without or with one decollement, but no backthrusts was formed in the wedges with two decollements. Slow erosion allows lower extent of basal underthrusting in comparison with regular-rate erosion. Variations in the erosion taper lead to changes in duplex geometry and exhumation rate in thrust wedges with one or two decollements. The 6 degrees erosion taper promotes formation of antiformal stack at the rear part of thrust wedge, high rate of basal underthrusting and high extent of erosional removal. The cover layers are nearly completely eroded above the antiformal stack and form the synformal klippe in frontal part of thrust wedges. The 8 degrees erosion taper allows development of individual ramp-anticlines and active forward thrusting of cover layers above the decollement and low rate of basal underplating below it, with consequent low extent of erosional removal. The results of our experiments support the observations on structural evolution and erosion in the Alberta Foothills of the Canadian Rockies.
ISSN: 0040-1951

hal-00617769
https://hal.archives-ouvertes.fr/hal-00617769
DOI : 10.1016/j.tecto.2011.01.020

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
Chlordecone is an organochlorine pesticide that was extensively used in the French West Indies to fight weevils in banana plantations from 1973 to 1993. This has led to a persistent pollution of the environment and to the contamination of the local population for several decades with effects demonstrated on human health. Chlordecone accumulates mainly in the liver where it is known to potentiate the action of hepatotoxic agents. However, there is currently no information on its in situ localization in the liver. We have thus evaluated a matrix-assisted laser desorption ionization (MALDI) imaging quantification method based on labeled normalization for the in situ localization and quantification of chlordecone. After validating the linearity and the reproducibility of this method, quantitative MALDI imaging was used to study the accumulation of chlordecone in the mouse liver. Our results revealed that normalized intensities measured by MALDI imaging could be first converted in quantitative units. These quantities appeared to be different from absolute quantities of chlordecone determined by gas chromatography (GC), but they were perfectly correlated (R(2) = 0.995). The equation of the corresponding correlation curve was thus efficiently used to convert quantities measured by MALDI imaging into absolute quantities. Our method combining labeled normalization and calibration with an orthogonal technique allowed the in situ absolute quantification of chlordecone by MALDI imaging. Finally, our results obtained on the pathological mouse liver illustrate the advantages of quantitative MALDI imaging which preserves information on in situ localization without radioactive labeling and with a simple sample preparation.
ISSN: 0003-2700

hal-01118103
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118103
PUBMED : 24837422
DOI : 10.1021/ac500313s

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Evidence of the impact of exposure to low levels of lead on children's health is increasing. Residential floor dust is the assumed origin of lead exposure by young children. In this study, we estimate the contribution of different lead sources to household interior floor dust contamination. We also estimate the within-home variability of interior floor dust lead loadings. A multilevel model was developed based on data collected in a French survey in 2008-2009 (484 housing units, 1834 rooms). Missing data were handled by multiple imputation using chained equations. The intra-home correlation between interior floor Log dust lead loadings was approximately 0.6. Dust lead from the landing of an apartment, mostly originating outside the building, was the major contributor to interior floor dust lead. Secondary contributors included the lead-based paint on exterior railings, track-in of the exterior soil of the children's play area into the dwelling, smoking inside the home, demolition of nearby old buildings and sites of pollution in the vicinity. Interior lead-based paint contaminated interior floor dust only in old and non-renovated dwellings. To reduce interior floor dust lead levels in the general population of dwellings, common areas should be maintained, and track-in from the outside should be limited as much as possible.
ISSN: 0048-9697

hal-01017419
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01017419
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01017419/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01017419/file/Source_Contribution_final.pdf
DOI : 10.1016/j.scitotenv.2013.10.028

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We discuss various methods of regularization of singular differential problems. Their common point is that we use the flexibility of the theories of nonlinear generalized functions for adapting the regularization to the singularity of the problem. We particularly underline the relationship between the generalized solutions and those classical or distribution, when they exist, giving a general result for the case of the regularization of data.
Journal of Mathematical Analysis and applications

hal-01529550
https://hal.univ-antilles.fr/hal-01529550
DOI : 10.1016/j.jmaa.2008.11.077

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We show that a new definition of the asymptotic structure of the (C,E,P)-algebras (which are a refinement of the Colombeau Generalized Algebras) allows to define a natural topology on them. Furthermore, this topology can be mixed with functorial aspects of the construction in order to give extension principles, which give powerful tools to solve singular differential problems in this framework.
ISSN: 0022-247X

hal-01529551
https://hal.univ-antilles.fr/hal-01529551
DOI : 10.1016/j.jmaa.2009.05.046

Éditeur(s) : HAL CCSD International Publishing Service/IPS
Résumé : International audience
We give a description of various algebras of generalized functions based on the introduction of pseudo-ultranorms on spaces of sequences in given locally convex function algebras. We study sheaf properties of these algebras, needed for microlocal analysis, and also consider regularity theory, functoriality and different concepts of association and weak equality in a unified setting. Using this approach, we also give new results on embeddings of ultradistribution and hyperfunction spaces into corresponding algebras of generalized functions.
ISSN: 0012-3862

hal-00758044
https://hal.univ-antilles.fr/hal-00758044
https://hal.univ-antilles.fr/hal-00758044/document
https://hal.univ-antilles.fr/hal-00758044/file/DHPV-26oct-8nov06.pdf
DOI : 10.4064/dm447-0-1

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional regions of the phase space close to which the dynamics is much slower compared to the rest of the phase space. These metastable regimes depend on the network topology and on the orders of magnitude of the kinetic parameters. Benchmarking of the method on a computational biology model repository suggests that the number of metastable regimes is sub-exponential in the number of variables and equations. The dynamics of the network can be described as a sequence of jumps from one metastable regime to another. We show that a geometrically computed con-nectivity graph restricts the set of possible jumps. We also provide finite state machine (Markov chain) models for such dynamic changes. Applied to signal transduction models, our approach unravels dynamical and functional * corresponding author capacities of signalling pathways, as well as parameters responsible for speci-ficity of the pathway response. In particular, for a model of TGFβ signalling, we find that the ratio of TGFBR2 to TGFBR1 receptors concentrations can be used to discriminate between metastable regimes. Using expression data from the NCI60 panel of human tumor cell lines, we show that aggressive and non-aggressive tumour cell lines function in different metastable regimes and can be distinguished by measuring the relative concentrations of receptors of the two types.
ISSN: 0303-2647

hal-01379033
https://hal.inria.fr/hal-01379033
https://hal.inria.fr/hal-01379033/document
https://hal.inria.fr/hal-01379033/file/Samal_et_al_Biosystems_final.pdf
DOI : 10.1016/j.biosystems.2016.07.004

Éditeur(s) : HAL CCSD Kluwer Academic Publishers
Résumé : International audience
The interlocking leaves of tank-forming bromeliads (Bromeliaceae) collect rainwater and detritus, thus creating a freshwater habitat for specialized organisms. Their abundance and the possibility of quantifying communities with accuracy give us unparalleled insight into how changes in local to regional environments influence community diversity in small water bodies. We sampled 365 bromeliads (365 invertebrate communities) along a southeastern to northwestern range in French Guiana. Geographic locality determined the species pool for bromeliad invertebrates, and local environments determined the abundance patterns through the selection of traits that are best adapted to the bromeliad habitats. Patterns in community structure mostly emerged from patterns of predator species occurrence and abundance across local-regional environments, while the set of detritivores remained constant. Water volume had a strong positive correlation with invertebrate diversity, making it a biologically relevant measure of the pools' carrying capacity. The significant effects of incoming detritus and incident light show that changes in local environments (e.g., the conversion of forest to cropping systems) strongly influence freshwater communities. Because changes in local environments do not affect detritivores and predators equally, one may expect functional shifts as sets of invertebrates with particular traits are replaced or complemented by other sets with different traits.
Hydrobiologia

hal-00845572
https://hal.archives-ouvertes.fr/hal-00845572

Éditeur(s) : HAL CCSD Elsevier
Résumé : The correct characterization of the effective reactive transport dynamics is an important issue for modeling reactive transport on the Darcy scale, specifically in situations in which reactions are localized, that is when different reactions occur in different portions of the porous medium. Under such conditions the conventional approach of homogenizing only the porous medium chemistry is not appropriate. We consider here reactive transport in a porous medium that is characterized by mass transfer between a mobile and a distribution of immobile regions. Chemical and physical heterogeneities are reflected by distributions of kinetic reaction rate constants and residence times in the immobile zones. We derive an effective reactive transport equation for the mobile solute that is characterized by non-local physical mass transfer and reaction terms. Specifically, chemical heterogeneity is upscaled in terms of a reactive memory function that integrates both chemical and physical heterogeneity. Mass transfer limitations due to physical heterogeneity yield effective kinetic rate coefficients that can be much smaller than the volumetric average of the local scale coefficients. These results help to explain and quantify the often reported discrepancy between observed field reaction rate constants and the ones obtained under well mixed laboratory conditions. Furthermore, these results indicate that transport under physical and chemical heterogeneity cannot be upscaled separately.
ISSN: 0169-7722

hal-00617674
https://hal.archives-ouvertes.fr/hal-00617674
DOI : 10.1016/j.jconhyd.2010.06.002

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : 51 pages; 15figures; 3 tables, accepted for publication in PloS ONE
International audience
We present a study about AFM imaging of living, moving or self-immobilized, bacteria in their genuine physiological liquid medium. No external immobilization protocol, neither chemical nor mechanical, was needed. For the first time, the native gliding movements of Gram-negative Nostoc cyanobacteria upon the surface, at speeds up to 900microns/h, were studied by AFM. This was possible thanks to an improved combination of a gentle sample preparation process and an AFM procedure based on fast and complete force-distance curves made at every pixel, drastically reducing lateral forces. No limitation in spatial resolution or imaging rate was detected. Gram-positive and non-motile R. wratislaviensis bacteria were studied as well. From the approach curves, Young modulus and turgor pressure were measured for both strains at different gliding speeds and are ranging from 20±3 to 105±5MPa and 40±5 to 310±30kPa depending on the bacterium and the gliding speed. For Nostoc, spatially limited zones with higher values of stiffness were observed. The related spatial period is much higher than the mean length of Nostoc nodules. This was explained by an inhomogeneous mechanical activation of nodules in the Nostoc. We also observed the presence of a soft extra cellular matrix (ECM) around the Nostoc. Both strains left a track of polymeric slime with variable thicknesses. For R. wratislaviensis, it is equal to few hundreds of nanometers, likely to promote its adhesion to the sample. While gliding, the Nostoc secretes a slime layer the thickness of which is in the nanometer range and increases with the gliding speed.
ISSN: 1932-6203

hal-00769765
https://hal.archives-ouvertes.fr/hal-00769765
https://hal.archives-ouvertes.fr/hal-00769765v3/document
https://hal.archives-ouvertes.fr/hal-00769765/file/REsubmission_In-situ_determination_Dhahri_Plos_One_R2_Hal.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : The Gulf of Aigues-Mortes (NW Mediterranean Sea) is a midshelf zone whose scale is an intermediate between the nearshore scale (0–10 m depth) and the coastal scale (including the whole continental shelf). Its hydrodynamics is investigated for the first time. ADCP, CTD and thermosalinograph data were collected during three short cruises (HYGAM; March 6–7, 20–21, April 5–6, 2005). They were scheduled approximately every 15 days to sample the gulf circulation under different weather conditions. Moreover, the cruise data were used to validate the Symphonie model, a 3D primitive equations circulation model. The circulation features displayed by in situ data were well reproduced by Symphonie. A downscaling modelling approach was implemented, the largest scale being obtained by the replay of the MFSTEP regional model of the North-Western Mediterranean Sea. The analysis, closely coupling in situ measurements and model results, provides information that would not have been obtained using data separately. The great variability of the oceanic circulation at this scale is well evidenced. Winds are the main forces, not only locally but also at a larger scale. North winds generate coherent structures interacting with the general Mediterranean circulation. The explanation of the induced currents is then not straightforward, some of them being, for example, northward. South and southeast winds reinforce the sloping surface, the latter allowing the geostrophic equilibrium with longshore currents. This study, focused on the end of winter 2004–2005, also enhances the heat fluxes from offshore to nearshore, as well as the initiation of shelf dense waters. The knowledge of the midshelf oceanic circulation is then applied to run a numerical experiment which describes both the dispersion of a fictive contaminant from a point S (at the centre of the GAM), and evaluates the risk of contamination of the beaches along the GAM shores.
ISSN: 0278-4343

hal-00196620
https://hal.archives-ouvertes.fr/hal-00196620
DOI : 10.1016/j.csr.2007.06.006

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : International audience
The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalence between bulk phase and single-molecule approaches, or the relationships between single-cycle transient probabilities and steady state rates. Twelve methods proposed by different authors and yielding the same famous Michaelis-Menten equation, are selected here to illustrate the kinetic and probabilistic use of rate constants and to review basic techniques for handling them. Finally, the general rate of an ordered multistep reaction, of which the Michaelis-Menten reaction is a particular case, is deduced from a Markovian approach.
ISSN: 0259-9791

hal-00920806
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00920806
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00920806v2/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00920806/file/12MM.pdf
ARXIV : 1312.5468

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Individuals can play different roles in maintaining connectivity and socialcohesion in animal populations and thereby influence population robustnessto perturbations.We performed a social network analysis in a reef shark populationto assess the vulnerability of the global network to node removal underdifferent scenarios. We found that the network was generally robust to theremoval of nodes with high centrality. The network appeared also highlyrobust to experimental fishing. Individual shark catchability decreased as afunction of experience, as revealed by comparing capture frequency and sitepresence. Altogether, these features suggest that individuals learnt to avoidcapture, which ultimately increased network robustness to experimentalcatch-and-release. Our results also suggest that some caution must be takenwhen using capture–recapture models often used to assess population sizeas assumptions (such as equal probabilities of capture and recapture) maybe violated by individual learning to escape recapture.
EISSN: 1471-2954

hal-01561754
https://hal-univ-perp.archives-ouvertes.fr/hal-01561754
DOI : 10.1098/rsbl.2016.0824

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We conducted triaxial compression experiments to investigate the effects of pressure, temperature and strain rate on the rheology of talc rocks. The tests were carried out at T from 25 to 860 degrees C, P from 0.1 to 300 MPa, and <(epsilon) over dot> from 0.3 to 30 x 10-5 s(-1). In addition to being very weak, there are other important differences between the mechanical behavior of talc and that of most other silicates. Deformation at all temperatures up to dehydration was accommodated by a combination of crystal plasticity, frictional sliding, and cataclasis. A transition from localized to distributed deformation occurred at P = 300 MPa and T = 400 degrees C, but this transition is ill-defined as both distributed and localized deformation were observed at P = 300 MPa and T = 600 degrees C. Unlike most silicates, both the coefficient of internal friction and the coefficient of (sliding) friction are very low and nearly equal to each other. Temperature enhances plastic deformation (kinking), and inter- and intra-granular microcracks are observed parallel to the (001) planes at all conditions. Voids are created by delamination along (001) planes at kink-band boundaries. Full crystal plasticity was not achieved under any of the conditions tested, i.e., the von Mises criterion was never satisfied. However, the strength of the aggregates remained much less than the confining pressure. These unusual properties are likely a manifestation of the pronounced mechanical anisotropy of talc at the grain scale. At T >= 750 degrees C dehydration is observed, but only along shear zones. These results suggest that feedbacks between deformation and reaction kinetics could control fluid flow in fault zones. The presence of talc can promote significant weakening and strain localization in the oceanic lithosphere, the subducting plate and the overlying mantle wedge. (c) 2008 Elsevier B.V. All rights reserved.
ISSN: 0012-821X

hal-00492706
https://hal.archives-ouvertes.fr/hal-00492706
DOI : 10.1016/j.epsl.2008.02.004

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
TIF1γ (Transcriptional Intermediary Factor 1 γ) has been implicated in Smad-dependent signaling by Transforming Growth Factor beta (TGF-β). Paradoxically, TIF1γ functions both as a transcriptional repressor or as an alternative transcription factor that promotes TGF-β signaling. Using ordinary differential-equation models, we have investigated the effect of TIF1γ on the dynamics of TGF-β signaling. An integrative model that includes the formation of transient TIF1γ-Smad2-Smad4 ternary complexes is the only one that can account for TGF-β signaling compatible with the different observations reported for TIF1γ. In addition, our model predicts that varying TIF1γ/Smad4 ratios play a critical role in the modulation of the transcriptional signal induced by TGF-β, especially for short stimulation times that mediate higher threshold responses. Chromatin immunoprecipitation analyses and quantification of the expression of TGF-β target genes as a function TIF1γ/Smad4 ratios fully validate this hypothesis. Our integrative model, which successfully unifies the seemingly opposite roles of TIF1γ, also reveals how changing TIF1γ/Smad4 ratios affect the cellular response to stimulation by TGF-β, accounting for a highly graded determination of cell fate.
ISSN: 1932-6203

hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483/document
https://hal.archives-ouvertes.fr/hal-00851483/file/pone.0033761.pdf
DOI : 10.1371/journal.pone.0033761

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This article is devoted to the presentation of a multilevel method using finite differences that is well adapted for solving Stokes and Navier-Stokes problems in primitive variables. We use Uzawa type algorithms to solve the saddle point problems arising from spatial discretization by staggered grids and a semi-explicit temporal scheme. By means of a new change of basis operator, the two-dimensional velocity and pressure fields of an M.A.C mesh are gathered in a hierarchical order, into several grids preserving the M.A.C property on each of them. These new hierarchical unknowns, called Staggered Incremental Unknowns (SIU), allow us to develop techniques which reduce the cost of the resolution of either Stokes or generalized Stokes problems. An experimental estimation of the condition number of the inner matrix is given, and justifies the preconditioning effect of the staggered incremental unknowns.
ISSN: 0168-9274

hal-00770268
https://hal.univ-antilles.fr/hal-00770268
DOI : 10.1016/S0168-9274(99)00044-6

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Dynamic Bifurcations

hal-01529542
https://hal.univ-antilles.fr/hal-01529542