laboratoire de physique statistique
laboratoire de physique statistique




P A R M I :

Why must visual stimuli be so poor? - Ninio, J.
PERCEPTION 4160 (2012)
Peristaltic patterns for swelling and shrinking of soft cylindrical gels - Ciarletta, Pasquale and Ben Amar, Martine
SOFT MATTER 81760-1763 (2012)

Abstract : We propose a variational method for determining the surface patterns of cylindrical gels for both swelling and shrinking. Exact solutions are calculated for the initial stages of such peristaltic instabilities. The morphology and the formation mechanisms depend on a competition between bulk elastic energy and surface tension.
Mechanical Instabilities of Gels - Dervaux, Julien and Ben Amar, Martine

Abstract : Although the study of gels undoubtedly takes its roots within the field of physicochemistry, the interest in gels has flourished and they have progressively become an important object in the study of the mechanics of polymeric materials and volumetric growth, raising some fascinating problems, some of them remaining unsolved. Because gels are multiphase objects, their study represents an important step in the understanding of the mechanics of complex soft matter as well as for the process of shape generation in biological bodies. The scope of this article is to review the understanding we have of the mechanical behavior of gels, with a strong focus on the development of instabilities in swelling gels.
Approaches to the Study of Atg8-Mediated Membrane Dynamics In Vitro - Jotwani, Anjali and Richerson, Diana N. and Motta, Isabelle and Julca-Zevallos, Omar and Melia, Thomas J.
in LIPIDS, VOL 108 edited by DiPaolo, G and Wenk, MR (2012)

Abstract : Macro-autophagy is the intracellular stress-response pathway by which the cell packages portions of the cytosol for delivery into the lysosome. This ``packaging'' is carried out by the de novo formation of a new organelle called the autophagosome that grows and encapsulates cytosolic material for eventual lysosomal degradation. How autophagosomes form, including especially how the membrane expands and eventually closes upon itself is an area of intense study. One factor implicated in both membrane expansion and membrane fusion is the ubiquitin-like protein, Atg8. During autophagy, Atg8 becomes covalently bound to phosphatidylethanolamine (PE) on the pre-autophagosomal membrane and remains bound through the maturation process of the autophagosome. In this chapter, we discuss two approaches to the in vitro reconstitution of this lipidation reaction. We then describe methods to study Atg8-PE mediated membrane tethering and fusion, two functions implicated in Atg8's role in autophagosome maturation.
Pattern formation by dewetting and evaporating sedimenting suspensions - Habibi, Mehdi and Moller, Peder and Fall, Abdoulaye and Rafai, Salima and Bonn, Daniel
SOFT MATTER 84682-4686 (2012)

Abstract : Pattern formation from drying droplets containing sedimenting particles and dewetting of thin films of such suspensions was studied. The dewetting causes the formation of finger-like patterns near the contact line which leave behind a deposit of branches. We find that the strikingly low speed of dewetting is due to the high particle concentration in the contact line region, leading to a strongly enhanced viscosity. For pattern formation from drying droplets (containing particles), evaporation also causes dewetting. In both cases, we find a similar relationship between the size of the patterns and the dewetting speed. The coefficient of this relationship gives us the effective viscosity at the contact line. We present a simple model that accounts for this, and that shows that the size of the particles is the relevant length scale in both problems.
Shear thickening of Laponite suspensions with poly(ethylene oxide) - Fall, Abdoulaye and Bonn, Daniel
SOFT MATTER 84645-4651 (2012)

Abstract : We study the effect of addition of polyethylene oxide (PEO) on the rheological behavior of suspensions of Laponite. Experiments were performed on mixtures of PEO and Laponite at different concentrations. These mixtures can exhibit very strong shear thickening behavior: under shear, the suspension can become a yield stress material sufficiently strong to support its own weight. Depending on the polymer concentration, we observe continuous or discontinuous shear thickening mechanisms; it is the discontinuous shear thickening that leads to the formation of yield stress materials.
How genealogies are affected by the speed of evolution - Brunet, Eric and Derrida, Bernard

Abstract : In a series of recent works it has been shown that a class of simple models of evolving populations under selection leads to genealogical trees whose statistics are given by the Bolthausen-Sznitman coalescent rather than by the well-known Kingman coalescent in the case of neutral evolution. Here we show that when conditioning the genealogies on the speed of evolution, one finds a one-parameter family of tree statistics which interpolates between the Bolthausen-Sznitman and Kingman coalescents. This interpolation can be calculated explicitly for one specific version of the model, the exponential model. Numerical simulations of another version of the model and a phenomenological theory indicate that this one-parameter family of tree statistics could be universal. We compare this tree structure with those appearing in other contexts, in particular in the mean field theory of spin glasses.
Dynamical heterogeneity in aging colloidal glasses of Laponite - Jabbari-Farouji, S. and Zargar, R. and Wegdam, G. H. and Bonn, Daniel
SOFT MATTER 85507-5512 (2012)

Abstract : Glasses behave as solids due to their long relaxation time; however the origin of this slow response remains a puzzle. Growing dynamic length scales due to cooperative motion of particles are believed to be central to the understanding of both the slow dynamics and the emergence of rigidity. Here, we provide experimental evidence of a growing dynamical heterogeneity length scale that increases with increasing waiting time in an aging colloidal glass of Laponite. The signature of heterogeneity in the dynamics follows from dynamic light scattering measurements in which we study both the rotational and translational diffusion of the disk-shaped particles of Laponite in suspension. These measurements are accompanied by simultaneous microrheology and macroscopic rheology experiments. We find that rotational diffusion of particles slows down at a faster rate than their translational motion. Such decoupling of translational and orientational degrees of freedom finds its origin in the dynamic heterogeneity since rotation and translation probe different length scales in the sample. The macroscopic rheology experiments show that the low frequency shear viscosity increases at a much faster rate than both rotational and translational diffusive relaxation times.
Liquid Rope Coiling - Ribe, Neil M. and Habibi, Mehdi and Bonn, Daniel
in ANNUAL REVIEW OF FLUID MECHANICS, VOL 44 edited by Davis, SH and Moin, P (2012)

Abstract : A thin stream or rope of viscous fluid falling from a sufficient height onto a surface forms a steadily rotating helical coil. Tabletop laboratory experiments in combination with a numerical model for slender liquid ropes reveal that finite-amplitude coiling can occur in four distinct regimes (viscous, gravitational, inertio-gravitational, and inertial) corresponding to different balances among the three principal forces acting on the rope. The model further shows that the onset of coiling has distinct viscous, gravitational, and inertial modes that connect smoothly with the corresponding finite-amplitude regimes. In addition to steady coiling, slender liquid ropes falling onto surfaces can exhibit a remarkable variety of nonstationary behaviors, including propagating spiral waves of air bubbles, supercoiling, the leaping-shampoo (Kaye) effect for non-Newtonian fluids, and the fluid-mechanical sewing machine in which the rope leaves complex stitch patterns on a moving surface.
Reversals of a large-scale field generated over a turbulent background - Gallet, B. and Herault, J. and Laroche, C. and Petrelis, F. and Fauve, S.

Abstract : We present a study of several systems in which a large-scale field is generated over a turbulent background. These large-scale fields break a symmetry of the forcing by selecting a direction. Under certain conditions, the large-scale field displays reversals so that the symmetry of the forcing is recovered statistically. We present examples of such dynamics in the context of the dynamo instability, of two-dimensional turbulent Kolmogorov flows and of turbulent Rayleigh-Benard convection. In these systems reversals occur respectively for the dynamo magnetic field, for the large-scale circulation generated by a periodic forcing in space and for the large-scale roll generated by turbulent thermal convection. We compare the mechanisms involved and show that their properties depend on some symmetries of the system and on the way they are broken.
Interaction between polarons and analogous effects in polarized Fermi gases - Giraud, S. and Combescot, R.

Abstract : We consider an imbalanced mixture of two different ultracold Fermi gases, which are strongly interacting. Calling spin-down the minority component and spin-up the majority component, the limit of small relative density x = n(down arrow)/n(up arrow) is usually considered as a gas of noninteracting polarons. This allows us to calculate, in the expansion of the total energy of the system in powers of x, the terms proportional to x (corresponding to the binding energy of the polaron) and to x(5/3) (corresponding to the kinetic energy of the polaron Fermi sea). We investigate in this paper terms physically due to an interaction between polarons and which are proportional to x(2) and x(7/3). We find three such terms. The first one corresponds to the overlap between the clouds dressing two polarons. The two other ones are due to the modification of the single polaron binding energy caused by the nonzero density of polarons. The second term is due to the restriction of the polaron momentum by the Fermi sea formed by the other polarons. The last one results from the modification of the spin-up Fermi sea brought by the other polarons. The calculation of all these terms is made at the simplest level of a single particle-hole excitation. It is performed for all the possible interaction strengths within the stability range of the polaron. At unitarity the last two terms give a fairly weak contribution while the first one is strong and leads to a marked disagreement with Monte Carlo results. The possible origins of this discrepancy are discussed.
Anomalous Exponents at the Onset of an Instability - Petrelis, F. and Alexakis, A.

Abstract : Critical exponents are calculated exactly at the onset of an instability, by using asymptotic expansion techniques. When the unstable mode is subject to multiplicative noise whose spectrum at zero frequency vanishes, we show that the critical behavior can be anomalous; i.e., the mode amplitude X scales with departure from onset mu as < X > proportional to mu(beta) with an exponent beta different from its deterministic value. This behavior is observed in a direct numerical simulation of the dynamo instability, and our results provide a possible explanation for recent experimental observations.
Detection and Quantification through a Lipid Membrane Using the Molecularly Controlled Semiconductor Resistor - Bavli, Danny and Tkachev, Maria and Piwonski, Hubert and Capua, Eyal and de Albuquerque, Ian and Bensimon, David and Haran, Gilad and Naaman, Ron
LANGMUIR 281020-1028 (2012)

Abstract : The detection of covalent and noncovalent binding events between molecules and biomembranes is a fundamental goal of contemporary biochemistry and analytical chemistry. Currently, such studies are performed routinely using fluorescence methods, surface-plasmon resonance spectroscopy, and electrochemical methods. However, there is still a need for novel sensitive miniaturizable detection methods where the sample does not have to be transferred to the sensor, but the sensor can be brought into contact with the sample studied. We present a novel approach for detection and quantification of processes occurring on the surface of a lipid bilayer membrane, by monitoring the current change through the n-type GaAs-based molecularly controlled semiconductor resistor (MOCSER), on which the membrane is adsorbed. Since GaAs is susceptible to etching in an aqueous environment, a protective thin film of methoxysilane was deposited on the device. The system was found to be sensitive enough to allow monitoring changes in pH and in the concentration of amino acids in aqueous solution on top of the membrane. When biotinylated lipids were incorporated into the membrane, it was possible to monitor the binding of streptavidin or avidin. The device modified with biotin-streptavidin complex was capable of detecting the binding of streptavidin antibodies to immobilized streptavidin with high sensitivity and selectivity. The response depends on the charge on the analyte. These results open the way to facile electrical detection of protein membrane interactions.
Polymerase Exchange During Okazaki Fragment Synthesis Observed in Living Cells (Retracted, see vol 346, pg 1466, 2014) - Lia, Giuseppe and Michel, Benedicte and Allemand, Jean-Francois
SCIENCE 335328-331 (2012)

Abstract : DNA replication machineries have been studied extensively, but the kinetics of action of their components remains largely unknown. We report a study of DNA synthesis during replication in living Escherichia coli cells. Using single-molecule microscopy, we observed repetitive fluorescence bursts of single polymerase IIIs (Pol IIIs), indicating polymerase exchange at the replication fork. Fluctuations in the amount of DNA-bound single-stranded DNA-binding protein (SSB) reflect different speeds for the leading-and lagging-strand DNA polymerases. Coincidence analyses of Pol III and SSB fluctuations show that they correspond to the lagging-strand synthesis and suggest the use of a new Pol III for each Okazaki fragment. Based on exchanges involving two Pol IIIs, we propose that the third polymerase in the replisome is involved in lagging-strand synthesis.
Perception of categories: From coding efficiency to reaction times - Bonnasse-Gahot, Laurent and Nadal, Jean-Pierre
BRAIN RESEARCH 143447-61 (2012)

Abstract : Reaction-times in perceptual tasks are the subject of many experimental and theoretical studies. With the neural decision making process as main focus, most of these works concern discrete (typically binary) choice tasks, implying the identification of the stimulus as an exemplar of a category. Here we address issues specific to the perception of categories (e.g. vowels, familiar faces,...), making a clear distinction between identifying a category (an element of a discrete set) and estimating a continuous parameter (such as a direction). We exhibit a link between optimal Bayesian decoding and coding efficiency, the latter being measured by the mutual information between the discrete category set and the neural activity. We characterize the properties of the best estimator of the likelihood of the category, when this estimator takes its inputs from a large population of stimulus-specific coding cells. Adopting the diffusion-to-bound approach to model the decisional process, this allows to relate analytically the bias and variance of the diffusion process underlying decision making to macroscopic quantities that are behaviorally measurable. A major consequence is the existence of a quantitative link between reaction times and discrimination accuracy. The resulting analytical expression of mean reaction times during an identification task accounts for empirical facts, both qualitatively (e.g. more time is needed to identify a category from a stimulus at the boundary compared to a stimulus lying within a category), and quantitatively (working on published experimental data on phoneme identification tasks). (C) 2011 Elsevier B.V. All rights reserved.
Lateral Diffusion and Association of Transmembrane Proteins Inside a Biomimetic Bilayer Mesophase - Rayan, Gamal and Reffay, Myriam and Picard, Martin and Taulier, Nicolas and Ducruix, Arnaud and Urbach, Wladimir
Chaotic motors - Laroche, C. and Labbe, R. and Petrelis, F. and Fauve, S.

Abstract : We show that electric motors and dynamos can be used to illustrate most elementary instabilities or bifurcations discussed in courses on nonlinear oscillators and dynamical systems. These examples are easier to understand and display a richer behavior than the ones commonly used from mechanics, electronics, hydrodynamics, lasers, chemical reactions, and population dynamics. In particular, an electric motor driven by a dynamo can display stationary, Hopf, and codimension-two bifurcations by tuning the driving speed of the dynamo and the electric current in the stator of the electric motor. When the dynamo is driven at constant torque instead of constant rotation rate, chaotic reversals of the generated current and of the angular rotation of the motor are observed. Simple deterministic models are presented which capture the observed dynamical regimes. (C) 2012 American Association of Physics Teachers.
Aggregation on a membrane of particles undergoing active exchange with a reservoir - Foret, L.

Abstract : We investigate the dynamics of clusters made of aggregating particles on a membrane which exchanges particles with a reservoir. Exchanges are driven by chemical reactions which supply energy to the system, leading to the establishment of a non-equilibrium steady state. We predict the distribution of cluster size at steady state. We show in particular that in a regime, that cannot exist at equilibrium, the distribution is bimodal: the membrane is mainly populated of single particles and finite-size clusters. This work is motivated by the observations that have revealed the existence of submicrometric clusters of proteins in biological membranes.
Different Cell Fates from Cell-Cell Interactions: Core Architectures of Two-Cell Bistable Networks - Rouault, Herve and Hakim, Vincent
BIOPHYSICAL JOURNAL 102417-426 (2012)

Abstract : The acquisition of different fates by cells that are initially in the same state is central to development. Here, we investigate the possible structures of bistable genetic networks that can allow two identical cells to acquire different fates through cell-cell interactions. Cell-autonomous bistable networks have been previously sampled using an evolutionary algorithm. We extend this evolutionary procedure to take into account interactions between cells. We obtain a variety of simple bistable networks that we classify into major subtypes. Some have long been proposed in the context of lateral inhibition through the Notch-Delta pathway, some have been more recently considered and others appear to be new and based on mechanisms not previously considered. The results highlight the role of posttranscriptional interactions and particularly of protein complexation and sequestration, which can replace cooperativity in transcriptional interactions. Some bistable networks are entirely based on posttranscriptional interactions and the simplest of these is found to lead, upon a single parameter change, to oscillations in the two cells with opposite phases. We provide qualitative explanations as well as mathematical analyses of the dynamical behaviors of various created networks. The results should help to identify and understand genetic structures implicated in cell-cell interactions and differentiation.
Dynamic interfacial tension effects in the rupture of liquid necks - Saint Vincent, M. Robert de and Petit, J. and Aytouna, M. and Delville, J. P. and Bonn, D. and Kelly, H.

Abstract : By examining the rupture of fluid necks during droplet formation of surfactant-laden liquids, we observe deviations from expected behaviour for the pinch-off of such necks. We suggest that these deviations are due to the presence of a dynamic (time-varying) interfacial tension at the minimum neck location and extract this quantity from our measurements on a variety of systems. The presence of such dynamic interfacial tension effects should change the rupture process drastically. However, our measurements show that a simple ansatz, which incorporates the temporal change of the interfacial tension, allows us to understand the dynamics of thinning. This shows that this dynamics is largely independent of the exact details of what happens far from the breakup location, pointing to the local nature of the thinning dynamics.