Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We study diffusion in a heterogeneous medium that is characterized by spatially varying diffusion properties from a random walk point of view. We show that an inhomogeneous continuous time random walk (CTRW) with a spatially variable exponential transition time distribution solves the spatially discretized heterogeneous diffusion equation. This demonstrates the equivalence of the widely used time-domain random walk (TDRW) scheme and spatially inhomogeneous CTRW and at the same time provides a demonstration of the formal equivalence of the TDRW particle formulation and the heterogeneous diffusion equation. Based on this equivalence, we develop a TDRW method for heterogeneous diffusion under spatially variable multirate mass transfer properties. We discuss the implementation of these schemes and study the diffusion behavior in the presence of traps that are characterized by a truncated power-law trapping time distribution.
ISSN: 0309-1708

hal-00767566
https://hal.archives-ouvertes.fr/hal-00767566
DOI : 10.1016/j.advwatres.2012.07.015

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Several studies, both theoretical and experimental, show that sedimentary rocks have a fractal pore-grain interface. In this paper a computer simulated 3-D sedimentary rock structure generated by the Relaxed Ballistic Bidisperse Deposition Model (RBBDM), is investigated to characterize the micro structure of its pores. The pore volume and the rock-pore interface show the same fractal dimension indicating that the pore volume is a fractal. The two point density correlation is computed for the pore space and the results compare favourably with the range reported from experiments. An array of 2-D X-ray tomography micrograph sections of a real sedimentary rock, an oolitic limestone (pure calcite) from the Mondeville formation of Middle Jurassic age (Paris Basin, France), was used to generate a 3-D bitmap. The 3-D real rock sample generated in this manner, was analysed for similar studies as the simulated structure. The results were compared with those obtained from simulation. The simulation results agree qualitatively with the real rock sample. Diffusion through the connected pore space of the simulated structure was studied using a random walk algorithm and the results compared with the similar simulation study done on the 3-D oolitic limestone specimen. In both cases diffusion was found to be anomalous indicating that the sedimentary rock has a fractal geometry. The favourable comparability of results between the simulated and real rock supports the usefulness of the model of sedimentary rock generation which can be applicable to transport phenomena.
ISSN: 0956-540X

hal-00823061
https://hal.archives-ouvertes.fr/hal-00823061
DOI : 10.1093/gji/ggs084

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Random walk (RW) or Continuous Time Random Walk (CTRW) are recurring Monte Carlo methods used to model convective and diffusive transport in complex heterogeneous media. Many applications can be found, including fluid mechanic, hydrology, and chemical reactors modeling. These methods are easy to implement, very versatile and flexible enough to become appealing for many applications because they generally overlook of deeply simplify the building of explicit complex meshes required by deterministic methods. RW and CTRW provide a good physical understanding of the interactions between the space scales of het-erogeneities and the transport phenomena under consideration. In addition, they can result in efficient up-scaling methods, especially in context of flow and transport in fractured media. In the present study, we review the applications of RW or CTRW for several situations coping with various spatial scales, and different insights into up-scaling applications. RW and CTRW advantages and downsides are also discussed, thus providing a few avenues for further works and applications.
ISSN: 0169-3913

hal-01449131
https://hal.archives-ouvertes.fr/hal-01449131
https://hal.archives-ouvertes.fr/hal-01449131/document
https://hal.archives-ouvertes.fr/hal-01449131/file/0025972-02.pdf
DOI : 10.1007/s11242-016-0693-z

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
We derive a general formulation of the time domain random walk (TDRW) approach to model the hydrodynamic transport of inert solutes in complex geometries and heterogeneous media. We demonstrate its formal equivalence with the discretized advection-dispersion equation and show that the TDRW is equivalent to a continuous time random walk (CTRW) characterized by space-dependent transition times and transition probabilities. The transition times are exponentially distributed. We discuss the implementation of different concentration boundary conditions and initial conditions as well as the occurrence of numerical dispersion. Furthermore, we propose an extension of the TDRW scheme to account for mobile-immobile multirate mass transfer. Finally, the proposed TDRW scheme is validated by comparison to analytical solutions for spatially homogeneous and heterogeneous transport scenarios.
ISSN: 0043-1397

hal-01356319
https://hal.archives-ouvertes.fr/hal-01356319
DOI : 10.1002/2015WR018511

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 American Geophysical Union
Résumé : International audience
Both flow field heterogeneity and mass transfer between mobile and immobile domains have been studied separately for explaining observed anomalous transport. Here we investigate non-Fickian transport using high-resolution 3-D X-ray microtomographic images of Berea sandstone containing microporous cement with pore size below the setup resolution. Transport is computed for a set of representative elementary volumes and results from advection and diffusion in the resolved macroporosity (mobile domain) and diffusion in the microporous phase (immobile domain) where the effective diffusion coefficient is calculated from the measured local porosity using a phenomenological model that includes a porosity threshold ( inline image) below which diffusion is null and the exponent n that characterizes tortuosity-porosity power-law relationship. We show that both flow field heterogeneity and microporosity trigger anomalous transport. Breakthrough curve (BTC) tailing is positively correlated to microporosity volume and mobile-immobile interface area. The sensitivity analysis showed that the BTC tailing increases with the value of inline image, due to the increase of the diffusion path tortuosity until the volume of the microporosity becomes negligible. Furthermore, increasing the value of n leads to an increase in the standard deviation of the distribution of effective diffusion coefficients, which in turn results in an increase of the BTC tailing. Finally, we propose a continuous time random walk upscaled model where the transition time is the sum of independently distributed random variables characterized by specific distributions. It allows modeling a 1-D equivalent macroscopic transport honoring both the control of the flow field heterogeneity and the multirate mass transfer between mobile and immobile domains.
ISSN: 0043-1397

hal-01278285
https://hal.archives-ouvertes.fr/hal-01278285
DOI : 10.1002/2015WR017645

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Random walk (RW) methods are recurring Monte Carlo methods used to modelconvective and diffusive transport in complex heterogeneous media. Many applications canbe found, including fluid mechanic, hydrology and chemical reactors modeling. These methodsare easy to implement, very versatile and flexible enough to become appealing for manyapplications because they generally overlook or deeply simplify the building of explicit complexmeshes required by deterministic methods. RWprovides a good physical understandingof the interactions between the space scales of heterogeneities and the transport phenomenaunder consideration. In addition, they can result in efficient upscaling methods, especiallyin the context of flow and transport in fractured media. In the present study, we review theapplications of RW to several situations that cope with diverse spatial scales and differentinsights into upscaling problems. The advantages and downsides of RW are also discussed,thus providing a few avenues for further works and applications.
ISSN: 0169-3913

insu-01308060
https://hal-insu.archives-ouvertes.fr/insu-01308060
DOI : 10.1007/s11242-016-0693-z

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In this paper, we have presented a spectral and a multifractal analysis performed on 412 time series of wind speed data each of duration of 350 s and sampled at 20 Hz. The average spectrum for the wind speed displays a scaling behavior, in the inertial range, over two decades, with b ¼ 1:68 close to the Kolmogorov value À 5/3. A multifractal analysis has been motivated by the presence of scaling invariance in data set. Then we have considered their scaling properties in the framework of fully developed turbulence and multifractal cascades. The results obtained for wind speed confirm that the exponent scaling function z V ðqÞ is nonlinear and concave. This exponent characterizes the scaling functions in the inertial range indicating that the wind speed is intermittent and multifractal. Moreover the theoretical quadratic relation for lognormal multifractals is well fitted. We investigate the consequence for wind energy production: we generate stochastic simulations of a multifractal random walk, and using a power curve derived from experimental data, we generate the associated power time series. We show that, due to the saturation of the power curve for large speed values, when the input time series (turbulent wind speed) is multifractal, the output can be almost monofractal.
ISSN: 0167-6105

hal-01527886
https://hal.archives-ouvertes.fr/hal-01527886
DOI : 10.1016/j.jweia.2012.06.002

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely preadapted molecules, selected on the basis of their affinity in one-step associations. But the counterselection of inappropriate interactions can in fact be much more efficiently obtained through difficult multi-step adjustment, whose final high energy state is locked by a fluctuation ratchet. The progressive addition of molecular bonds during stereo-adjustment can be modeled as a predominantly backward random walk whose first arrival is frozen by a micro-irreversible transition. A new criterion of ligand specificity is presented, that is based on the ratio rejection/incorporation. In addition to its role in the selectivity of interactions, this generic recipe can underlie other important biological phenomena such as the regular synthesis at low level of supramolecular complexes, monostable kinetic bimodality, substrate concentration thresholds or the preparation of rapidly depolymerizable structures with stored energy, like microtubules
ISSN: 0079-6107

hal-01274234
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01274234
DOI : 10.1016/j.pbiomolbio.2016.02.001
PUBMED : 26867859

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
Mobile-immobile mass transfer is widely used to model non-Fickian dispersion in porous media. Nevertheless, the memory function, implemented in the sink/source term of the transport equation to characterize diffusion in the matrix (i.e., the immobile domain), is rarely measured directly. Therefore, the question can be posed as to whether the memory function is just a practical way of increasing the degrees of freedom for fitting tracer test breakthrough curves or whether it actually models the physics of tracer transport. In this paper we first present a technique to measure the memory function of aquifer samples and then compare the results with the memory function fitted from a set of field-scale tracer tests performed in the same aquifer. The memory function is computed by solving the matrix diffusion equation using a random walk approach. The properties that control diffusion (i.e., mobile-immobile interface and immobile domain cluster shapes, porosity, and tortuosity) are investigated by X-ray microtomography. Once the geometry of the matrix clusters is measured, the shape of the memory function is controlled by the value of the porosity at the percolation threshold and of the tortuosity of the diffusion path. These parameters can be evaluated from microtomographic images. The computed memory function compares well with the memory function deduced from the field-scale tracer tests. We conclude that for the reservoir rock studied here, the atypical non-Fickian dispersion measured from the tracer test is well explained by microscale diffusion processes in the immobile domain. A diffusion-controlled mobileimmobile mass transfer model therefore appears to be valid for this specific case.
ISSN: 0043-1397

insu-00373705
https://hal-insu.archives-ouvertes.fr/insu-00373705
https://hal-insu.archives-ouvertes.fr/insu-00373705/document
https://hal-insu.archives-ouvertes.fr/insu-00373705/file/Gouze_et_al-2008-Water_Resources_Research.pdf
DOI : 10.1029/2007WR006690

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 (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 American Geophysical Union
Résumé : International audience
We aim at testing and validating a mobile-immobile mass transfer model from a set of single-well injection withdrawal tracer tests in a heterogeneous porous aquifer. By varying the duration of the injection phase, different volumes of aquifer are investigated by the tracer. Hence, we focus the transport model validation not only on reproducing a single breakthrough curve (BTC) but also on the model's capacity to predict the amount of mixing as a function of the volume visited by the tracer. All the BTCs are strongly asymmetric, as expected when dispersion is controlled by diffusive mass transfers between the mobile water and the immobile water part of the porosity. However, the BTC cannot be modeled by a conventional mobile-immobile mass transfer model with a simple power law memory function. To account for that, we implement a continuous time random walk model in which the transition time distribution y (t), which is related to the excursion time probability of the tracer in the immobile domain, is a dual-slope power law distribution. The model best fits the BTC data set with a transitional regime controlled by y(t) t2 and an asymptotic regime characteristic of the conventional double-porosity model with y(t) t1.5 . This work emphasizes that high-resolution concentration measurement and multiple-scale tracer tests are required for assessing solute dispersion models in heterogeneous reservoirs and for subsequently obtaining reliable predictions.
ISSN: 0043-1397

insu-00373698
https://hal-insu.archives-ouvertes.fr/insu-00373698
https://hal-insu.archives-ouvertes.fr/insu-00373698/document
https://hal-insu.archives-ouvertes.fr/insu-00373698/file/Borgne_et_al-2008-Water_Resources_Research.pdf
DOI : 10.1029/2007WR006279

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 (IMFs) using Empirical Mode Decomposition (EMD). We use a new approach, arbitrary order Hilbert spectral analysis, a combination of the EMD approach with Hilbert spectral analysis (or Hilbert-Huang Transform) and the classical structure-function analysis to extract the scaling exponents or multifractal spectrum ζ(q)ζ(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, gives 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-00846643
https://hal.archives-ouvertes.fr/hal-00846643
DOI : 10.1016/j.physa.2013.04.038

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. Seven 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.
Journal of Mathematical Chemistry

hal-00920806
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00920806
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00920806/document
ARXIV : 1312.5468
DOI : 10.1007/s10910-013-0237-5

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND: There is no recommendation for treating pulmonary hypertension (PH) when associated with chronic obstructive pulmonary disease (COPD). OBJECTIVE: To evaluate the effect of PH-specific therapy in patients with COPD. METHODS: All successive patients with severe PH [mean pulmonary arterial pressure (mPAP) ≥35 mm Hg] and COPD, who received specific PH medication and who underwent right heart catheterization at baseline and after 3-12 months of treatment, were analyzed from a prospective database. RESULTS: Twenty-six patients were included with a median follow-up of 14 months. Mean forced expiratory volume in 1 s was 57 ± 20% of predicted, and mean forced expiratory volume in 1 s/forced vital capacity was 47 ± 12%. Dyspnea was New York Health Association classification stage (NYHA) II in 15%, NYHA III in 81% and NYHA IV in 4%. First-line treatments were endothelin receptor antagonists in 11 patients, phosphodiesterase-5 inhibitors in 11 patients, calcium blocker in 1 patient, combination therapy in 3 patients including 2 with a prostanoid. After 6 ± 3 months, pulmonary vascular resistance decreased from 8.5 ± 3 to 6.6 ± 2 Wood units (p extless 0.001), with significant improvement of cardiac index from 2.44 ± 0.43 to 2.68 ± 0.63 liters × min × m-2 (p = 0.015) and mPAP from 48 ± 9 to 42 ± 10 mm Hg (p = 0.008). There was no significant difference in dyspnea, 6-min walking distance, echocardiographic parameters or N-terminal pro-brain natriuretic peptide levels. There was no significant difference in arterial oxygen saturation after 3-12 months of treatment. CONCLUSIONS: Specific PH medications may improve hemodynamic parameters in COPD patients with severe PH. Appropriate prospective randomized studies are needed to evaluate the potential long-term clinical benefit of treatment
Respiration; International Review of Thoracic Diseases

hal-01239807
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01239807
DOI : 10.1159/000431380
PUBMED : 26277885

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In this paper, we have presented a spectral and a multifractal analysis performed on 412 time series of wind speed data each of duration of 350 s and sampled at 20 Hz. The average spectrum for the wind speed displays a scaling behavior, in the inertial range, over two decades, with β=1.68 close to the Kolmogorov value −5/3. A multifractal analysis has been motivated by the presence of scaling invariance in data set. Then we have considered their scaling properties in the framework of fully developed turbulence and multifractal cascades. The results obtained for wind speed confirm that the exponent scaling function ζV(q) is nonlinear and concave. This exponent characterizes the scaling functions in the inertial range indicating that the wind speed is intermittent and multifractal. Moreover the theoretical quadratic relation for lognormal multifractals is well fitted. We investigate the consequence for wind energy production: we generate stochastic simulations of a multifractal random walk, and using a power curve derived from experimental data, we generate the associated power time series. We show that, due to the saturation of the power curve for large speed values, when the input time series (turbulent wind speed) is multifractal, the output can be almost monofractal.
ISSN: 0167-6105

hal-00779049
https://hal.archives-ouvertes.fr/hal-00779049
DOI : 10.1016/j.jweia.2012.06.002