laboratoire de physique statistique
laboratoire de physique statistique


The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis - Six, Adrien and Mariotti-Ferrandiz, Maria Encarnita and Chaara, Wahiba and Magadan, Susana and Hang-Phuong Pham and Lefranc, Marie-Paule and Mora, Thierry and Thomas-Vaslin, Veronique and Walczak, Aleksandra M. and Boudinot, Pierre

Abstract : T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a ``next-generation'' of repertoire analysis.
High-Reynolds-number turbulence in complex fluids - Kulmatova, D. and Bonn, D. and Kellay, H.
EPL 101 (2013)

Abstract : We here examine the structure of turbulence in the case of a complex fluid made up of water and surfactants. This fluid has the particular property of shear thickening when driven at shear rates above a certain threshold. Through a study of the spectral properties and the structure function scalings, important differences arise with respect to the reference case, i.e., water. The surfactant solution shows strong intermittency at small scales. The large scales are, on the other hand, free of intermittency. While this transition is observed in the structure function scalings, no sign of this transition is seen in the power spectrum of velocity fluctuations which shows a single scaling range. The strongly intermittent small-scale region, despite the scaling of the power spectrum, exhibits properties reminiscent of the near-dissipative range. Copyright (C) EPLA, 2013
Genealogies in simple models of evolution - Brunet, Eric and Derrida, Bernard

Abstract : We review the statistical properties of the genealogies of a few models of evolution. In the asexual case, selection leads to coalescence times which grow logarithmically with the size of the population, in contrast with the linear growth of the neutral case. Moreover for a whole class of models, the statistics of the genealogies are those of the Bolthausen-Sznitman coalescent rather than the Kingman coalescent in the neutral case. For sexual reproduction in the neutral case, the time to reach the first common ancestors for the whole population and the time for all individuals to have all their ancestors in common are also logarithmic in the population size, as predicted by Chang in 1999. We discuss how these times are modified by introducing selection in a simple way.
Theoretical analysis of growth or swelling wrinkles on constrained soft slabs - Jia, Fei and Ben Amar, Martine
SOFT MATTER 98216-8226 (2013)

Abstract : Growth or swelling of soft slabs attached to a rigid substrate generates large compressive stresses at their surfaces. When the stresses exceed a critical value, the smooth surface becomes unstable. For an in-plane isotropic material, a nonlinear three dimensional analysis is employed to ascertain the energy in the buckled state for different modes: stripes, squares and hexagons. When increasing the growth control parameter, we show that hexagonal patterns with a dimple at the center minimize the elastic energy and will be the dominant mode if the mode with minimal energy is the most likely to be observed. The growth of an anisotropic material reinforced by fibers is also considered. The results provide a way to understand surface wrinkling patterns induced by equi-biaxial growth or swelling of elastic layers, with possible applications for micro-patterns fabrication through an appropriate fiber arrangement.
Viscous fingering at ultralow interfacial tension - Setu, Siti Aminah and Zacharoudiou, Ioannis and Davies, Gareth J. and Bartolo, Denis and Moulinet, Sebastien and Louis, Ard A. and Yeomans, Julia M. and Aarts, Dirk G. A. L.
SOFT MATTER 910599-10605 (2013)

Abstract : We experimentally study the viscous fingering instability in a fluid-fluid phase separated colloid-polymer mixture by means of laser scanning confocal microscopy and microfluidics. We focus on three aspects of the instability. (i) The interface between the two demixed phases has an ultralow surface tension, such that we can address the role of thermal interface fluctuations. (ii) We image the interface in three dimensions allowing us to study the interplay between interface curvature and flow. (iii) The displacing fluid wets all walls completely, in contrast to traditional viscous fingering experiments, in which the displaced fluid wets the walls. We also perform lattice Boltzmann simulations, which help to interpret the experimental observations.
Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization - Menoret, Delphine and Santolini, Marc and Fernandes, Isabelle and Spokony, Rebecca and Zanet, Jennifer and Gonzalez, Ignacio and Latapie, Yvan and Ferrer, Pierre and Rouault, Herve and White, Kevin P. and Besse, Philippe and Hakim, Vincent and Aerts, Stein and Payre, Francois and Plaza, Serge

Abstract : Background: Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known about how the ultimate effectors of cell differentiation are selected and controlled. We addressed this question during late Drosophila embryogenesis, when the finely tuned expression of the TF Ovo/Shavenbaby (Svb) triggers the morphological differentiation of epidermal trichomes. Results: We defined a sizeable set of genes downstream of Svb and used in vivo assays to delineate 14 enhancers driving their specific expression in trichome cells. Coupling computational modeling to functional dissection, we investigated the regulatory logic of these enhancers. Extending the repertoire of epidermal effectors using genome-wide approaches showed that the regulatory models learned from this first sample are representative of the whole set of trichome enhancers. These enhancers harbor remarkable features with respect to their functional architectures, including a weak or non-existent clustering of Svb binding sites. The in vivo function of each site relies on its intimate context, notably the flanking nucleotides. Two additional cis-regulatory motifs, present in a broad diversity of composition and positioning among trichome enhancers, critically contribute to enhancer activity. Conclusions: Our results show that Svb directly regulates a large set of terminal effectors of the remodeling of epidermal cells. Further, these data reveal that trichome formation is underpinned by unexpectedly diverse modes of regulation, providing fresh insights into the functional architecture of enhancers governing a terminal differentiation program.
Thin Films in Complete Wetting and the Specific Case of Nematic Liquid Crystals - Cazabat, A. M. and Delabre, U. and Richard, C. and Sang, Y. Yip Cheung
The BEC-BCS Crossover in Ultracold Fermi Gases - Combescot, R.
in FIFTY YEARS OF NUCLEAR BCS: PAIRING IN FINITE SYSTEMS edited by Broglia, RA and Zelevinsky, V (2013)

Abstract : We provide an introduction to the matter of ultracold Fermi gases and the observation of the BEC-BCS crossover in these systems. We discuss in particular the simple modelisation of these gases, the Fano-Feshbach resonance, the simple BCS model of the crossover, the equation of state at T = 0, experiments on superfluid vortices and on critical velocity, results with the T-matrix approximation, and the Fermi polaron.
Dynamic Stability of Crack Fronts: Out-Of-Plane Corrugations - Adda-Bedia, Mokhtar and Arias, Rodrigo E. and Bouchbinder, Eran and Katzav, Eytan

Abstract : The dynamics and stability of brittle cracks are not yet fully understood. Here we use the Willis-Movchan 3D linear perturbation formalism [J. Mech. Phys. Solids 45, 591 (1997)] to study the out-ofplane stability of planar crack fronts in the framework of linear elastic fracture mechanics. We discuss a minimal scenario in which linearly unstable crack front corrugations might emerge above a critical front propagation speed. We calculate this speed as a function of Poisson's ratio and show that corrugations propagate along the crack front at nearly the Rayleigh wave speed. Finally, we hypothesize about a possible relation between such corrugations and the long-standing problem of crack branching. DOI: 10.1103/PhysRevLett.110.014302
Giant Plasticity of a Quantum Crystal - Haziot, Ariel and Rojas, Xavier and Fefferman, Andrew D. and Beamish, John R. and Balibar, Sebastien

Abstract : When submitted to large stresses at high temperature, usual crystals may irreversibly deform. This phenomenon is known as plasticity and it is due to the motion of crystal defects such as dislocations. We have discovered that, in the absence of impurities and in the zero temperature limit, helium 4 crystals present a giant plasticity that is anisotropic and reversible. Direct measurements on oriented single crystals show that their resistance to shear nearly vanishes in one particular direction because dislocations glide freely parallel to the basal planes of the hexagonal structure. This plasticity disappears as soon as traces of helium 3 impurities bind to the dislocations or if their motion is damped by collisions with thermal phonons.
Drop Formation in Non-Newtonian Fluids - Aytouna, Mounir and Paredes, Jose and Shahidzadeh-Bonn, Noushine and Moulinet, Sebastien and Wagner, Christian and Amarouchene, Yacine and Eggers, Jens and Bonn, Daniel

Abstract : We study the pinch-off dynamics of droplets of yield stress and shear thinning fluids. To separate the two non-Newtonian effects, we use a yield stress material for which the yield stress can be tuned without changing the shear thinning behavior, and a shear thinning system (without a yield stress) for which the shear thinning can be controlled over a large range, without introducing too much elasticity into the system. We find that the pinch-off remains very similar to that of constant viscosity Newtonian liquids, and consequently thinning in shear flow does not imply a thinning in elongational flow.
Exact solution of a Levy walk model for anomalous heat transport - Dhar, Abhishek and Saito, Keiji and Derrida, Bernard

Abstract : The Levy walk model is studied in the context of the anomalous heat conduction of one-dimensional systems. In this model, the heat carriers execute Levy walks instead of normal diffusion as expected in systems where Fourier's law holds. Here we calculate exactly the average heat current, the large deviation function of its fluctuations, and the temperature profile of the Levy walk model maintained in a steady state by contact with two heat baths (the open geometry). We find that the current is nonlocally connected to the temperature gradient. As observed in recent simulations of mechanical models, all the cumulants of the current fluctuations have the same system-size dependence in the open geometry. For the ring geometry, we argue that a size-dependent cutoff time is necessary for the Levy walk model to behave like mechanical models. This modification does not affect the results on transport in the open geometry for large enough system sizes. DOI: 10.1103/PhysRevE.87.010103
Direct Observation of Stalled Fork Restart and Lesion Bypass via Fork Regression in the T4 Replication System - Croquette, Vincent and Manosas, Maria and Perumal, Senthil K. and Benkovic, Stephen J.
A New Biomimetic Phase of Surfactant Bilayers Maintains Membrane Protein Activity - Adrien, Vladimir and Rayan, Gamal and Reffay, Myriam and Picard, Martin and Ducruix, Arnaud and Maldonado, Amir and Porcar, Lionel and Taulier, Nicolas and Urbach, Wladimir
Ideal evolution of magnetohydrodynamic turbulence when imposing Taylor-Green symmetries - Brachet, M. E. and Bustamante, M. D. and Krstulovic, G. and Mininni, P. D. and Pouquet, A. and Rosenberg, D.

Abstract : We investigate the ideal and incompressible magnetohydrodynamic (MHD) equations in three space dimensions for the development of potentially singular structures. The methodology consists in implementing the fourfold symmetries of the Taylor-Green vortex generalized to MHD, leading to substantial computer time and memory savings at a given resolution; we also use a regridding method that allows for lower-resolution runs at early times, with no loss of spectral accuracy. One magnetic configuration is examined at an equivalent resolution of 6144(3) points and three different configurations on grids of 4096(3) points. At the highest resolution, two different current and vorticity sheet systems are found to collide, producing two successive accelerations in the development of small scales. At the latest time, a convergence of magnetic field lines to the location of maximum current is probably leading locally to a strong bending and directional variability of such lines. A novel analytical method, based on sharp analysis inequalities, is used to assess the validity of the finite-time singularity scenario. This method allows one to rule out spurious singularities by evaluating the rate at which the logarithmic decrement of the analyticity-strip method goes to zero. The result is that the finite-time singularity scenario cannot be ruled out, and the singularity time could be somewhere between t = 2.33 and t = 2.70. More robust conclusions will require higher resolution runs and grid-point interpolation measurements of maximum current and vorticity.
Dimer-dimer scattering length for fermions with different masses: Analytical study for large mass ratio - Alzetto, F. and Combescot, R. and Leyronas, X.

Abstract : We study the dimer-dimer scattering length a(4) for a two-component Fermi mixture in which the different fermions have different masses m(up arrow) and m(down arrow). This is made in the framework of the exact field-theoretic method. In the large mass ratio domain the equations are simplified enough to lead to an analytical solution. In particular we link a(4) to the fermion-dimer scattering length a(3) for the same fermions and obtain the very simple relation a(4) = a(3)/2. The result a(4) similar or equal to a(3)/2 is actually valid whatever the mass ratio with quite good precision. As a result we find an analytical expression providing a(4) with fairly good precision for any mass. To dominant orders for large mass ratio it agrees with the literature. We show that in this large mass ratio domain, the dominant processes are the repeated dimer-dimer Born scatterings, considered earlier by Pieri and Strinati [Phys Rev. B 61, 15370 (2000)]. We conclude that their approximation of retaining only these processes is a fairly good one whatever the mass ratio. DOI: 10.1103/PhysRevA.87.022704
RecA-Promoted, RecFOR-Independent Progressive Disassembly of Replisomes Stalled by Helicase Inactivation (Retracted article. See vol. 54, pg. 537, 2014) - Lia, Giuseppe and Rigato, Annafrancesca and Long, Emilie and Chagneau, Carine and Le Masson, Marie and Allemand, Jean-Francois and Michel, Benedicte
MOLECULAR CELL 49547-557 (2013)

Abstract : In all organisms, replication impairment is a recognized source of genomic instability, raising an increasing interest in the fate of inactivated replication forks. We used Escherichia coli strains with a temperature-inactivated replicative helicase (DnaB) and in vivo single-molecule microscopy to quantify the detailed molecular processing of stalled replication forks. After helicase inactivation, RecA binds to blocked replication forks and is essential for the rapid release of hPol III. The entire holoenzyme is disrupted little by little, with some components lost in few minutes, while others are stable in 70\% of cells for at least 1 hr. Although replisome dissociation is delayed in a recA mutant, it is not affected by RecF or RecO inactivation. RecFOR are required for full RecA filaments formation, and we propose that polymerase clearance can be catalyzed by short, RecFOR-independent RecA filaments. Our results identify a function for the universally conserved, central recombination protein RecA.
Large-Scale Magnetic Fields in Magnetohydrodynamic Turbulence - Alexakis, Alexandros

Abstract : High Reynolds number magnetohydrodynamic turbulence in the presence of zero-flux large-scale magnetic fields is investigated as a function of the magnetic field strength. For a variety of flow configurations, the energy dissipation rate epsilon follows the scaling epsilon proportional to U-rms(3)/l even when the large-scale magnetic field energy is twenty times larger than the kinetic energy. A further increase of the magnetic energy showed a transition to the epsilon proportional to (UrmsBrms)-B-2/l scaling implying that magnetic shear becomes more efficient at this point at cascading the energy than the velocity fluctuations. Strongly helical configurations form nonturbulent helicity condensates that deviate from these scalings. Weak turbulence scaling was absent from the investigation. Finally, the magnetic energy spectra support the Kolmogorov spectrum k(-5/3) while kinetic energy spectra are closer to the Iroshnikov-Kraichnan spectrum k(-3/2) as observed in the solar wind. DOI: 10.1103/PhysRevLett.110.084502
Dislocation densities and lengths in solid He-4 from elasticity measurements - Haziot, Ariel and Fefferman, Andrew D. and Beamish, John R. and Balibar, Sebastien

Abstract : Measurements on solid He-4 show large softening of the shear modulus due to dislocations, behavior which has been described as giant plasticity. Dislocation networks may also be responsible for the unusual behavior seen in torsional oscillator and flow experiments. However, previous estimates of dislocation densities vary by many orders of magnitude, even in single crystals grown under similar conditions. By measuring the temperature and frequency dependencies of the elastic dissipation, we have determined dislocation densities and network lengths in 4He single crystals, both in coexistence with liquid and at higher pressures, and in polycrystals grown at constant density. In all cases, dislocation lengths are much longer and the networks are less connected than previous estimates. Even in polycrystals, the dislocation network is far too sparse to explain the torsional oscillator results in terms of superfluidity in a dislocation network. DOI:10.1103/PhysRevB.87.060509
The simplest maximum entropy model for collective behavior in a neural network - Tkacik, Gasper and Marre, Olivier and Mora, Thierry and Amodei, Dario and Berry, II, Michael J. and Bialek, William

Abstract : Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on capturing the measured correlations among pairs of neurons. Here we suggest an alternative, constructing models that are consistent with the distribution of global network activity, i.e. the probability that K out of N cells in the network generate action potentials in the same small time bin. The inverse problem that we need to solve in constructing the model is analytically tractable, and provides a natural `thermodynamics' for the network in the limit of large N. We analyze the responses of neurons in a small patch of the retina to naturalistic stimuli, and find that the implied thermodynamics is very close to an unusual critical point, in which the entropy (in proper units) is exactly equal to the energy.