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O Bénichou

Publications and source records attributed to O Bénichou.

17 recordsLinked to original sources
PubMed2006

Two-dimensional intermittent search processes: An alternative to Lévy flight strategies.

Lévy flights are known to be optimal search strategies in the particular case of revisitable targets. In the relevant situation of nonrevisitable targets, we propose an alternative model of two-dimensional (2D) search processes, which explicitly relies on the widely observed intermittent behavior of foraging animals. We show analytically that intermittent strategies can minimize the search time, and therefore do constitute real optimal strategies. We study two representative modes of target detection and determine which features of the search time are robust and do not depend on the specific characteristics of detection mechanisms. In particular, both modes lead to a global minimum of the search time as a function of the typical times spent in each state, for the same optimal duration of the ballistic phase. This last quantity could be a universal feature of 2D intermittent search strategies.

Journal Article↗
PubMed2005

First-passage times for random walks in bounded domains.

We present a novel computational method of first-passage times between a starting site and a target site of regular bounded lattices. We derive accurate expressions for all the moments of this first-passage time, validated by numerical simulations. Their range of validity is discussed. We also consider the case of a starting site and two targets. In addition, we present the extension to continuous Brownian motion. These results are of great relevance to any system involving diffusion in confined media.

Journal Article↗
PubMed2005

Kinetics of diffusion-limited catalytically activated reactions: an extension of the Wilemski-Fixman approach.

We study the kinetics of diffusion-limited catalytically activated A+B-->B reactions taking place in three-dimensional systems, in which an annihilation of diffusive A particles by diffusive traps B may happen only if the encounter of an A with any of the Bs happens within a special catalytic subvolumen: these subvolumens being immobile and uniformly distributed within the reaction bath. Suitably extending the classical approach of Wilemski and Fixman [J. Chem. Phys. 58, 4009 (1973)] to such three-molecular diffusion-limited reactions, we calculate analytically an effective reaction constant and show that it comprises several terms associated with the residence and joint residence times of Brownian paths in finite domains. The effective reaction constant exhibits a nontrivial dependence on the reaction radii, the mean density of catalytic subvolumens, and particles' diffusion coefficients. Finally, we discuss the fluctuation-induced kinetic behavior in such systems.

Adsorption↗
PubMed2005

First-exit times and residence times for discrete random walks on finite lattices.

In this paper, we derive explicit formulas for the surface averaged first-exit time of a discrete random walk on a finite lattice. We consider a wide class of random walks and lattices, including random walks in a nontrivial potential landscape. We also compute quantities of interest for modeling surface reactions and other dynamic processes, such as the residence time in a subvolume, the joint residence time of several particles, and the number of hits on a reflecting surface.

Journal Article↗
PubMed2005

Optimal search strategies for hidden targets.

What is the fastest way of finding a randomly hidden target? Experimental observations reveal that the search behavior of foraging animals is generally intermittent: active search phases randomly alternate with phases of fast ballistic motion. Here, we study the efficiency of this two state search strategy by calculating analytically the mean first passage time at the target. We model the perception mechanism involved in the active search phase by a diffusive process. We show that the search strategy is optimal when the average duration of "motion phases" varies like the power either 3/5 or 2/3 of the average duration of "search phases" depending on the regime. This scaling accounts for experimental data over a wide range of species, which suggests that the kinetics of search trajectories is a determining factor optimized by foragers and that the perception activity is adequately described by a diffusion process.

Journal Article↗
PubMed2004

Lattice theory of trapping reactions with mobile species.

We present a stochastic lattice theory describing the kinetic behavior of trapping reactions A+B-->B, in which both the A and B particles perform an independent stochastic motion on a regular hypercubic lattice. Upon an encounter of an A particle with any of the B particles, A is annihilated with a finite probability; finite reaction rate is taken into account by introducing a set of two-state random variables--"gates," imposed on each B particle, such that an open (closed) gate corresponds to a reactive (passive) state. We evaluate here a formal expression describing the time evolution of the A particle survival probability, which generalizes our previous results. We prove that for quite a general class of random motion of the species involved in the reaction process, for infinite or finite number of traps, and for any time t, the A particle survival probability is always larger in the case when A stays immobile, than in situations when it moves.

Journal Article↗
PubMed2004

Catalytic reactions with bulk-mediated excursions: mixing fails to restore chemical equilibrium.

In this paper we analyze the effect of the bulk-mediated excursions (BME) of reactive species on the long-time behavior of the catalytic Langmuir-Hinshelwood-like A+B-->0 reactions in systems in which a catalytic plane (CP) is in contact with a liquid phase, containing concentrations of reactive particles. Such BME result from repeated particles desorption from the CP, subsequent diffusion in the liquid phase, and eventual readsorption on the CP away from the initial detachment point. This process leads to an effective superdiffusive transport along the CP. We consider both "batch" reactions, in which all particles of reactive species were initially adsorbed onto the CP, and reactions followed by a steady inflow of particles onto the CP. We show that for batch reactions the BME provide an effective mixing channel and here the mean-field-type behavior emerges. On the contrary, for reaction followed by a steady inflow of particles, we observe essential departures from the mean-field behavior and find that the mixing effect of the BME is insufficient to restore chemical equilibrium. We show that a steady state is established as t--> infinity, in which the limiting value of the mean coverage of the CP depends on the particles' diffusion coefficient in the bulk liquid phase, and that the spatial distributions of adsorbed particles are strongly correlated. Moreover, we show that the relaxation to such a steady state is a power-law function of time, in contrast to the exponential time dependence describing the approach to equilibrium in perfectly stirred systems.

Journal Article↗
PubMed2004

Kinetics of target site localization of a protein on DNA: a stochastic approach.

It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders-of-magnitude faster than the maximal one calculated from the diffusion-limited theory. It was therefore commonly assumed that the target site interaction of a restriction enzyme with DNA has to occur via two steps: one-dimensional diffusion along a DNA segment, and long-range jumps coming from association-dissociation events. We propose here a stochastic model for this reaction which comprises a series of one-dimensional diffusions of a restriction enzyme on nonspecific DNA sequences interrupted by three-dimensional excursions in the solution until the target sequence is reached. This model provides an optimal finding strategy which explains the fast association rate. Modeling the excursions by uncorrelated random jumps, we recover the expression of the mean time required for target site association to occur given by Berg et al. in 1981, and we explicitly give several physical quantities describing the stochastic pathway of the enzyme. For competitive target sites we calculate two quantities: processivity and preference. By comparing these theoretical expressions to recent experimental data obtained for EcoRV-DNA interaction, we quantify: 1), the mean residence time per binding event of EcoRV on DNA for a representative one-dimensional diffusion coefficient; 2), the average lengths of DNA scanned during the one-dimensional diffusion (during one binding event and during the overall process); and 3), the mean time and the mean number of visits needed to go from one target site to the other. Further, we evaluate the dynamics of DNA cleavage with regard to the probability for the restriction enzyme to perform another one-dimensional diffusion on the same DNA substrate following a three-dimensional excursion.

Binding Sites↗
PubMed2003

Pascal principle for diffusion-controlled trapping reactions.

In this paper, we analyze the long-time behavior of the survival probability P(A)(t) of an A particle, that performs lattice random walk in the presence of randomly moving traps B. We show that for both perfect and imperfect trapping reactions, for arbitrary spatial dimension d and for a rather general class of random walks, P(A)(t) is less than or equal to the survival probability of an immobile target A in the presence of randomly moving traps.

Journal Article↗
PubMed2002

Trapping reactions with randomly moving traps: exact asymptotic results for compact exploration.

In a recent paper, Bray and Blythe have shown that the survival probability P(A)(t) of an A particle diffusing with a diffusion coefficient D(A) in a one-dimensional system with diffusive traps B is independent of D(A) in the asymptotic limit t--> infinity and coincides with the survival probability of an immobile target in the presence of diffusive traps. Here, we show that this remarkable behavior has a more general range of validity and holds for systems of an arbitrary dimension d, integer or fractal, provided that the traps are "compactly exploring" the space, i.e., the "fractal" dimension d(w) of traps' trajectories is greater than d. For the marginal case when d(w)=d, as exemplified here by conventional diffusion in two-dimensional systems, the decay form is determined up to a numerical factor in the characteristic decay time.

Journal Article↗
PubMed2002

Ultraslow vacancy-mediated tracer diffusion in two dimensions: the Einstein relation verified.

We study the dynamics of a charged tracer particle (TP) on a two-dimensional lattice, all sites of which except one (a vacancy) are filled with identical neutral, hard-core particles. The particles move randomly by exchanging their positions with the vacancy, subject to the hard-core exclusion. In the case when the charged TP experiences a bias due to external electric field E (which favors its jumps in the preferential direction), we determine exactly the limiting probability distribution of the TP position in terms of appropriate scaling variables and the leading large-n (n being the discrete time) behavior of the TP mean displacement X(n); the latter is shown to obey an anomalous, logarithmic law /X(n)/=alpha(0)(/E/)ln(n). Comparing our results with earlier predictions by Brummelhuis and Hilhorst [J. Stat. Phys. 53, 249 (1988)] for the TP diffusivity D(n) in the unbiased case, we infer that the Einstein relation mu(n)=betaD(n) between the TP diffusivity and the mobility mu(n)=lim(/E/-->0)(/X(n)///E/n) holds in the leading n order, despite the fact that both D(n) and mu(n) are not constant but vanish as n--> infinity. We also generalize our approach to the situation with very small but finite vacancy concentration rho(v), in which case we find a ballistic-type law /X(n)/=pi(alpha)(0)(/E/)rho(v)n. We demonstrate that here, again, both D(n) and mu(n), calculated in the linear in rho(v) approximation, do obey the Einstein relation.

Journal Article↗
PubMed2001

Albers-Schönberg disease (autosomal dominant osteopetrosis, type II) results from mutations in the ClCN7 chloride channel gene.

Albers-Schönberg disease, or autosomal dominant osteopetrosis, type II (ADO II), is the most common form of osteopetrosis, a group of conditions characterized by an increased skeletal mass due to impaired bone and cartilage resorption. Following the assignment of the gene causing ADO II to chromosome 16p13.3, we now report seven different mutations in the gene encoding the ClCN7 chloride channel in all 12 ADO II families analysed. Additionally, a patient with the severe, autosomal recessive, infantile form of osteopetrosis (ARO) was identified as being homozygous for a ClCN7 mutation. From genotype-phenotype correlations, it seems that ADO II reflects a dominant negative effect, whereas loss-of-function mutations in ClCN7 do not cause abnormalities in heterozygous individuals. Because some ARO patients have mutations in both copies of the ClCN7 gene, ADO II is allelic with a subset of ARO cases.

Alleles↗
PubMed2001

Atomic slide puzzle: self-diffusion of an impure atom.

In a series of recent papers [Phys. Rev. Lett. 86, 1562 (2001); Nature (London) 408, 665 (2000)] van Gastel and co-workers have presented what may be the first experimental evidence, based on a series of scanning tunnel microscope images, that impure, Indium atoms, embedded into the first, close-packed layer of a Cu(001) surface, are not localized but make concerted, long excursions. Such excursions occur due to continuous reshuffling of the surface following the position exchanges of both impure and host Cu atoms with the naturally occurring surface vacancies. van Gastel and co-workers have also formulated an original lattice-gas type model with asymmetric exchange probabilities, whose numerical solution is in a good agreement with the experimental data. In this paper we propose an exact lattice solution of several versions of this model.

Journal Article↗
PubMed2001

Mapping of autosomal dominant osteopetrosis type II (Albers-Schönberg disease) to chromosome 16p13.3.

The osteopetroses are a heterogeneous group of conditions characterized by a bone-density increase due to impaired bone resorption. As well as the two or more autosomal recessive types, two autosomal dominant forms of osteopetrosis, differentiated by clinical and radiological signs, are described. Autosomal dominant osteopetrosis (ADO) type II, also known as "Albers-Schönberg disease," is characterized by sclerosis, predominantly involving the spine (vertebral end-plate thickening, or Rugger-Jersey spine), the pelvis ("bone-within-bone" structures), and the skull base. An increased fracture rate can be observed in these patients. By linkage analysis, the presence, on chromosome 1p21, of a gene causing ADO type II was previously suggested. However, analysis of further families with ADO type II indicated genetic heterogeneity within ADO type II, with the chromosome 1p21 locus being only a minor locus. We now perform a genomewide linkage scan of a French extended family with ADO type II, which allows us to localize an ADO type II gene on chromosome 16p13.3. Analysis of microsatellite markers in five further families with ADO type II could not exclude this chromosomal region. A summed maximum LOD score of 12.70 was generated with marker D16S3027, at a recombination fraction (straight theta) of 0. On the basis of the key recombinants in the families, a candidate region of 8.4 cM could be delineated, flanked by marker D16S521, on distal side, and marker D16S423, on the proximal side. Surprisingly, one of the families analyzed is the Danish family previously suggested to have linkage to chromosome 1p21. Linkage to chromosome 16p13.3 clearly cannot be excluded in this family, since a maximum LOD score of 4.21 at theta=0 is generated with marker D16S3027. Because at present no other family with ADO type II has proved to have linkage to chromosome 1p21, we consider the most likely localization of the disease-causing gene in this family to be to chromosome 16p13.3. This thus reopens the possibility that ADO type II is genetically homogeneous because of a single gene on chromosome 16p13.3.

Chromosome Mapping↗
PubMed2001

Human osteopetrosis and other sclerosing disorders: recent genetic developments.

Osteopetroses are rare human genetic disorders due to markedly decreased bone resorption. To date, the only gene whose inactivation was known to be responsible for human osteopetroses was that encoding carbonic anhydrase type II. Recessive malignant osteopetrosis is linked to decreased osteoclast function, unlike several osteopetroses in rodents that are caused by the inactivation of genes stimulating osteoclast differentiation. Recent advances in genetics have shown that some patients affected with recessive malignant osteopetrosis have inactivating mutations in a subunit of the vacuolar proton pump that is actively produced in the osteoclast brush border, but not in the lysosomes of other cells. The same gene is mutated in osteopetrotic oc/oc mice. The genes responsible for autosomal dominant osteopetrosis (ADO) have not yet been identified. Also, different localizations have been observed for ADO II, the type with sandwich vertebrae, and ADO I, presenting with diffuse osteocondensation. Less data than in malignant osteopetrosis are avaible on the cellular mechanism of decreased bone resorption in ADO but there is also genetic heterogeneity in ADO II. Pycnodysostosis is also due to a decreased resorption, and is quite close to osteopetrosis. Pycnodysostosis is linked to an inactivating mutation in the gene encoding cathepsin K, which is required for osteoclastic resorption. Decreased bone resorption is not the only defect inducing osteosclerosis, and Camurati-Engelmann disease is due to increased bone formation. Recently it has been shown that it is associated with a mutation in the propeptide of TGFbeta1. Thus, human osteosclerosing disorders have a wide range of phenotypes and genotypes and knowledge of them will contribute to a better understanding of the remodeling of normal bone.

Animals↗
PubMed2000

[Physiopathology of bone loss and pharmacologic approach of selective estrogen receptor modulators].

Osteoclastic resorption increases at menopause and remains high during aging. The complex mechanism responsible for this increase involves cytokines and growth factors secreted by stromal cells and/or by osteoblasts and cells in the hematopoietic microenvironment. Although estrogen receptors have been found mainly on osteoblasts and their precursors, the stromal cells, they have also been demonstrated on osteoclast precursors. Raloxifene is a selective estrogen receptor modifier (SERM) that has the beneficial effects of estrogens on bone tissue but no estrogen agonist effects on the breast and uterus. Although recent data have established that the mechanism of action of estrogens and SERMs is far more complex than was previously thought, the reason for the tissue selectivity of these molecules remains unknown.

Animals↗