laboratoire de physique statistique
laboratoire de physique statistique




P A R M I :

Controlling molecular transport in minimal emulsions - Gruner, Philipp and Riechers, Birte and Semin, Benoit and Lim, Jiseok and Johnston, Abigail and Short, Kathleen and Baret, Jean-Christophe

Abstract : Emulsions are metastable dispersions in which molecular transport is a major mechanism driving the system towards its state of minimal energy. Determining the underlying mechanisms of molecular transport between droplets is challenging due to the complexity of a typical emulsion system. Here we introduce the concept of `minimal emulsions', which are controlled emulsions produced using microfluidic tools, simplifying an emulsion down to its minimal set of relevant parameters. We use these minimal emulsions to unravel the fundamentals of transport of small organic molecules in water-in-fluorinated-oil emulsions, a system of great interest for biotechnological applications. Our results are of practical relevance to guarantee a sustainable compartmentalization of compounds in droplet microreactors and to design new strategies for the dynamic control of droplet compositions.
One-dimensional collective migration of a proliferating cell monolayer - Recho, Pierre and Ranft, Jonas and Marcq, Philippe
SOFT MATTER 122381-2391 (2016)

Abstract : The importance of collective cellular migration during embryogenesis and tissue repair asks for a sound understanding of underlying principles and mechanisms. Here, we address recent in vitro experiments on cell monolayers, which show that the advancement of the leading edge relies on cell proliferation and protrusive activity at the tissue margin. Within a simple viscoelastic mechanical model amenable to detailed analysis, we identify a key parameter responsible for tissue expansion, and we determine the dependence of the monolayer velocity as a function of measurable rheological parameters. Our results allow us to discuss the effects of pharmacological perturbations on the observed tissue dynamics.
Time Delayed Equations as Models in Nature and Society - Guerrini, Luca and Gori, Luca and Matsumoto, Akio and Sodini, Mauro and Zhang, Zizhen and Bianca, Carlo
Statistical physics of inference: thresholds and algorithms - Zdeborova, Lenka and Krzakala, Florent
ADVANCES IN PHYSICS 65453-552 (2016)

Abstract : Many questions of fundamental interest in today's science can be formulated as inference problems: some partial, or noisy, observations are performed over a set of variables and the goal is to recover, or infer, the values of the variables based on the indirect information contained in the measurements. For such problems, the central scientific questions are: Under what conditions is the information contained in the measurements sufficient for a satisfactory inference to be possible? What are the most efficient algorithms for this task? A growing body of work has shown that often we can understand and locate these fundamental barriers by thinking of them as phase transitions in the sense of statistical physics. Moreover, it turned out that we can use the gained physical insight to develop new promising algorithms. The connection between inference and statistical physics is currently witnessing an impressive renaissance and we review here the current state-of-the-art, with a pedagogical focus on the Ising model which, formulated as an inference problem, we call the planted spin glass. In terms of applications we review two classes of problems: (i) inference of clusters on graphs and networks, with community detection as a special case and (ii) estimating a signal from its noisy linear measurements, with compressed sensing as a case of sparse estimation. Our goal is to provide a pedagogical review for researchers in physics and other fields interested in this fascinating topic.
Dynamical Analysis of a Computer Virus Model with Delays - Liu, Juan and Bianca, Carlo and Guerrini, Luca

Abstract : An SIQR computer virus model with two delays is investigated in the present paper. The linear stability conditions are obtained by using characteristic root method and the developed asymptotic analysis shows the onset of a Hopf bifurcation occurs when the delay parameter reaches a critical value. Moreover the direction of the Hopf bifurcation and stability of the bifurcating period solutions are investigated by using the normal form theory and the center manifold theorem. Finally, numerical investigations are carried out to show the feasibility of the theoretical results.
Critical behavior in the inverse to forward energy transition in two-dimensional magnetohydrodynamic flow - Seshasayanan, Kannabiran and Alexakis, Alexandros

Abstract : We investigate the critical transition from an inverse cascade of energy to a forward energy cascade in a two-dimensional magnetohydrodynamic flow as the ratio of magnetic to mechanical forcing amplitude is varied. It is found that the critical transition is the result of two competing processes. The first process is due to hydrodynamic interactions and cascades the energy to the large scales. The second process couples small-scale magnetic fields to large-scale flows, transferring the energy back to the small scales via a nonlocal mechanism. At marginality the two cascades are both present and cancel each other. The phase space diagram of the transition is sketched.
Fluctuating fitness shapes the clone-size distribution of immune repertoires - Desponds, Jonathan and Mora, Thierry and Walczak, Aleksandra M.

Abstract : The adaptive immune system relies on the diversity of receptors expressed on the surface of B-and T cells to protect the organism from a vast amount of pathogenic threats. The proliferation and degradation dynamics of different cell types (B cells, T cells, naive, memory) is governed by a variety of antigenic and environmental signals, yet the observed clone sizes follow a universal power-law distribution. Guided by this reproducibility we propose effective models of somatic evolution where cell fate depends on an effective fitness. This fitness is determined by growth factors acting either on clones of cells with the same receptor responding to specific antigens, or directly on single cells with no regard for clones. We identify fluctuations in the fitness acting specifically on clones as the essential ingredient leading to the observed distributions. Combining our models with experiments, we characterize the scale of fluctuations in antigenic environments and we provide tools to identify the relevant growth signals in different tissues and organisms. Our results generalize to any evolving population in a fluctuating environment.
Structures of Neural Correlation and How They Favor Coding - Franke, Felix and Fiscella, Michele and Sevelev, Maksim and Roska, Botond and Hierlemann, Andreas and da Silveira, Rava Azeredo
NEURON 89409-422 (2016)

Abstract : The neural representation of information suffers from ``noise''-the trial-to-trial variability in the response of neurons. The impact of correlated noise upon population coding has been debated, but a direct connection between theory and experiment remains tenuous. Here, we substantiate this connection and propose a refined theoretical picture. Using simultaneous recordings from a population of direction-selective retinal ganglion cells, we demonstrate that coding benefits from noise correlations. The effect is appreciable already in small populations, yet it is a collective phenomenon. Furthermore, the stimulus-dependent structure of correlation is key. We develop simple functional models that capture the stimulus-dependent statistics. We then use them to quantify the performance of population coding, which depends upon interplays of feature sensitivities and noise correlations in the population. Because favorable structures of correlation emerge robustly in circuits with noisy, nonlinear elements, they will arise and benefit coding beyond the confines of retina.
Transcriptional Memory in the Drosophila Embryo - Ferraro, Teresa and Esposito, Emilia and Mancini, Laure and Ng, Sam and Lucas, Tanguy and Coppey, Mathieu and Dostatni, Nathalie and Walczak, Aleksandra M. and Levine, Michael and Lagha, Mounia
CURRENT BIOLOGY 26212-218 (2016)

Abstract : Transmission of active transcriptional states from mother to daughter cells has the potential to foster precision in the gene expression programs underlying development. Such transcriptional memory has been specifically proposed to promote rapid reactivation of complex gene expression profiles after successive mitoses in Drosophila development [1]. By monitoring transcription in living Drosophila embryos, we provide the first evidence for transcriptional memory in animal development. We specifically monitored the activities of stochastically expressed transgenes in order to distinguish active and inactive mother cells and the behaviors of their daughter nuclei after mitosis. Quantitative analyses reveal that there is a 4-fold higher probability for rapid reactivation after mitosis when the mother experienced transcription. Moreover, memory nuclei activate transcription twice as fast as neighboring inactive mothers, thus leading to augmented levels of gene expression. We propose that transcriptional memory is a mechanism of precision, which helps coordinate gene activity during embryogenesis.
Different Buckling Regimes in Direct Electrospinning: A Comparative Approach to Rope Buckling - Shariatpanahi, S. P. and Etesami, Z. and Zad, A. Iraji and Bonn, D. and Ejtehadi, R.

Abstract : Understanding the dynamics of direct electrospinning is the key to control fiber morphologies that are critical for the development of new electrospinning methods and novel materials. Here, we propose the theory for direct electrospinning based on theories for (liquid) ``rope coiling'' and experimentally test it. For the experiments, the buckling of microscale liquid ropes formed from polymer solutions is studied systematically using three different electrospinning setups and for different polymer concentrations. We show that different buckling regimes exist, whose dynamics are governed by an interplay of electrical, inertial, and viscous forces, and that three different buckling regimes emerge depending on the dominant forces. For low polymer concentrations, we observe an inertial regime similar to that observed for viscous liquid ropes at high velocities. By increasing the polymer concentration and consequently decreasing the rope velocity, we enter an inertial-electrical regime for which discontinuities occur in the buckling frequency as a function of applied voltage. These observations can be accounted for quantitatively by replacing the gravitational forces in viscous rope coiling theory with the electrical forces of our electrospinning experiment. Finally, for the highest polymer concentration, we observe a purely electrical regime for a solidified rope; this regime is well described by ``elastic'' rope coiling theory. (c) 2015 Wiley Periodicals, Inc.
Contact gating at GHz frequency in graphene - Wilmart, Q. and Inhofer, A. and Boukhicha, M. and Yang, W. and Rosticher, M. and Morfin, P. and Garroum, N. and Feve, G. and Berroir, J. -M. and Placais, B.

Abstract : The paradigm of graphene transistors is based on the gate modulation of the channel carrier density by means of a local channel gate. This standard architecture is subject to the scaling limit of the channel length and further restrictions due to access and contact resistances impeding the device performance. We propose a novel design, overcoming these issues by implementing additional local gates underneath the contact region which allow a full control of the Klein barrier taking place at the contact edge. In particular, our work demonstrates the GHz operation of transistors driven by independent contact gates. We benchmark the standard channel and novel contact gating and report for the later dynamical transconductance levels at the state of the art. Our finding may find applications in electronics and optoelectronics whenever there is need to control independently the Fermi level and the electrostatic potential of electronic sources or to get rid of cumbersome local channel gates.
Experimental Measurement of the Activation Energy of Phospholipid Membrane Fusion - Francois-Martin, Claire and Rothman, James E. and Pincet, Frederic
Can We Trust Hydrodynamic Models to Determine the Bilayer Viscosity Experienced by Transmembrane Proteins? - Adrien, Vladimir and Astafyeva, Ksenia and Kuimova, Marina and Urbach, Wladimir and Taulier, Nicolas
Revisiting Sequencing by Hybridization at the Single Molecule Level using the Unzipping Assay - Croquette, Vincent and Raj, Saurabh and Allemand, Jean-Francois and Bensimon, David and Boule, Jean-Baptiste
Effect of a Cosolvent in Binding Events of Hydrophobic Molecules. An Experimental and Numerical Study - Senac, Caroline and Fuchs, Patrick and Urbach, Wladimir and Taulier, Nicolas
Remodeling of Gamete Membrane during Mammalian Fertilization - Ravaux, Benjamin and Gourier, Christine
Optimal Length Scale for a Turbulent Dynamo - Sadek, Mira and Alexakis, Alexandros and Fauve, Stephan

Abstract : We demonstrate that there is an optimal forcing length scale for low Prandtl number dynamo flows that can significantly reduce the required energy injection rate. The investigation is based on simulations of the induction equation in a periodic box of size 2 pi L. The flows considered are the laminar and turbulent ABC flows forced at different forcing wave numbers k(f), where the turbulent case is simulated using a subgrid turbulence model. At the smallest allowed forcing wave number k(f) = k(min) = 1/L the laminar critical magnetic Reynolds number Rm(c)(lam) is more than an order of magnitude smaller than the turbulent critical magnetic Reynolds number Rm(c)(turb) due to the hindering effect of turbulent fluctuations. We show that this hindering effect is almost suppressed when the forcing wave number k(f) is increased above an optimum wave number kfL similar or equal to 4 for which Rm(c)(turb) is minimum. At this optimal wave number, Rm(c)(turb) is smaller by more than a factor of 10 than the case forced in k(f) = 1. This leads to a reduction of the energy injection rate by 3 orders of magnitude when compared to the case where the system is forced at the largest scales and thus provides a new strategy for the design of a fully turbulent experimental dynamo.
Collective chemotaxis and segregation of active bacterial colonies - Ben Amar, M.

Abstract : Still recently, bacterial fluid suspensions have motivated a lot of works, both experimental and theoretical, with the objective to understand their collective dynamics from universal and simple rules. Since some species are active, most of these works concern the strong interactions that these bacteria exert on a forced flow leading to instabilities, chaos and turbulence. Here, we investigate the self-organization of expanding bacterial colonies under chemotaxis, proliferation and eventually active-reaction. We propose a simple model to understand and quantify the physical properties of these living organisms which either give cohesion or on the contrary dispersion to the colony. Taking into account the diffusion and capture of morphogens complicates the model since it induces a bacterial density gradient coupled to bacterial density fluctuations and dynamics. Nevertheless under some specific conditions, it is possible to investigate the pattern formation as a usual viscous fingering instability. This explains the similarity and differences of patterns according to the physical bacterial suspension properties and explain the factors which favor compactness or branching.
From cellular to tissue scales by asymptotic limits of thermostatted kinetic models - Bianca, Carlo and Dogbe, Christian and Lemarchand, Annie

Abstract : Tumor growth strictly depends on the interactions occurring at the cellular scale. In order to obtain the linking between the dynamics described at tissue and cellular scales, asymptotic methods have been employed, consisting in deriving tissue equations by suitable limits of mesoscopic models. In this paper, the evolution at the cellular scale is described by thermostatted kinetic theory that include conservative, nonconservative (proliferation, destruction and mutations), stochastic terms, and the role of external agents. The dynamics at the tissue scale (cell-density evolution) is obtained by performing a low-field scaling and considering the related convergence of the rescaled framework when the scaling parameter goes to zero.
On the Entropy of Protein Families - Barton, John P. and Chakraborty, Arup K. and Cocco, Simona and Jacquin, Hugo and Monasson, Remi

Abstract : Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely vary across organisms, giving rise to a protein family. Here, we estimate the entropy of those families based on different approaches, including Hidden Markov Models used for protein databases and inferred statistical models reproducing the low-order (1- and 2-point) statistics of multi-sequence alignments. We also compute the entropic cost, that is, the loss in entropy resulting from a constraint acting on the protein, such as the mutation of one particular amino-acid on a specific site, and relate this notion to the escape probability of the HIV virus. The case of lattice proteins, for which the entropy can be computed exactly, allows us to provide another illustration of the concept of cost, due to the competition of different folds. The relevance of the entropy in relation to directed evolution experiments is stressed.