laboratoire de physique statistique
 
 
laboratoire de physique statistique

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2016
DOI
21
On the Entropy of Protein Families - Barton, John P. and Chakraborty, Arup K. and Cocco, Simona and Jacquin, Hugo and Monasson, Remi
JOURNAL OF STATISTICAL PHYSICS 1621267-1293 (2016)

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.
DOI
22
JSP Special Issue on Information Processing in Living Systems - Mora, Thierry and Peliti, Luca and Rivoire, Olivier
JOURNAL OF STATISTICAL PHYSICS 1621085-1087 (2016)
DOI
23
Instability in electromagnetically driven flows. II - Imazio, Paola Rodriguez and Gissinger, Christophe
PHYSICS OF FLUIDS 28 (2016)

Abstract : In a previous paper, we have reported numerical simulations of the magnetohydrodynamic flow driven by a travelling magnetic field in an annular channel, at low Reynolds number. It was shown that the stalling of such induction pump is strongly related to magnetic flux expulsion. In the present article, we show that for larger hydrodynamic Reynolds number, and with more realistic boundary conditions, this instability takes the form of a large axisymmetric vortex flow in the (r, z)-plane, in which the fluid is locally pumped in the direction opposite to the one of the magnetic field. Close to the marginal stability of this vortex flow, a low-frequency pulsation is generated. Finally, these results are compared to theoretical predictions and are discussed within the framework of experimental annular linear induction electromagnetic pumps. (C) 2016 AIP Publishing LLC.
DOI
24
Instability in electromagnetically driven flows. I - Gissinger, Christophe and Imazio, Paola Rodriguez and Fauve, Stephan
PHYSICS OF FLUIDS 28 (2016)

Abstract : The magnetohydrodynamic flow driven by a travelling magnetic field in an annular channel is investigated numerically. For sufficiently large magnetic Reynolds number Rm, or if a large enough pressure gradient is externally applied, the system undergoes an instability in which the flow rate in the channel dramatically drops from synchronism with the wave to much smaller velocities. This transition takes the form of a saddle-node bifurcation for the time-averaged quantities. In this first paper, we characterize the bifurcation and study the stability of the flow as a function of several parameters. We show that the bifurcation of the flow involves a bistability between Poiseuille-like and Hartman-like regimes and relies on magnetic flux expulsion. Based on this observation, new predictions are made for the occurrence of this stalling instability. (C) 2016 AIP Publishing LLC.
DOI
25
Population aging through survival of the fit and stable - Brotto, Tommaso and Bunin, Guy and Kurchan, Jorge
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT  (2016)

Abstract : Motivated by the wide range of known self-replicating systems, some far from genetics, we study a system composed by individuals having an internal dynamics with many possible states that are partially stable, with varying mutation rates. Individuals reproduce and die with a rate that is a property of each state, not necessarily related to its stability, and the offspring is born on the parent's state. The total population is limited by resources or space, as for example in a chemostat or a Petri dish. Our aim is to show that mutation rate and fitness become more correlated, even if they are completely uncorrelated for an isolated individual, underlining the fact that the interaction induced by limitation of resources is by itself effcient for generating collective effects.
DOI
26
Elastic theory of origami-based metamaterials - Brunck, V. and Lechenault, F. and Reid, A. and Adda-Bedia, M.
PHYSICAL REVIEW E 93 (2016)

Abstract : Origami offers the possibility for new metamaterials whose overall mechanical properties can be programed by acting locally on each crease. Starting from a thin plate and having knowledge about the properties of the material and the folding procedure, one would like to determine the shape taken by the structure at rest and its mechanical response. In this article, we introduce a vector deformation field acting on the imprinted network of creases that allows us to express the geometrical constraints of rigid origami structures in a simple and systematic way. This formalism is then used to write a general covariant expression of the elastic energy of n-creases meeting at a single vertex. Computations of the equilibrium states are then carried out explicitly in two special cases: the generalized waterbomb base and the Miura-Ori. For the waterbomb, we show a generic bistability for any number of creases. For the Miura folding, however, we uncover a phase transition from monostable to bistable states that explains the efficient deployability of this structure for a given range of geometrical and mechanical parameters. Moreover, the analysis shows that geometric frustration induces residual stresses in origami structures that should be taken into account in determining their mechanical response. This formalism can be extended to a general crease network, ordered or otherwise, and so opens new perspectives for the mechanics and the physics of origami-based metamaterials.
DOI
27
Anomalous capillary filling and wettability reversal in nanochannels - Gravelle, Simon and Ybert, Christophe and Bocquet, Lyderic and Joly, Laurent
PHYSICAL REVIEW E 93 (2016)

Abstract : This work revisits capillary filling dynamics in the regime of nanometric to subnanometric channels. Using molecular dynamics simulations of water in carbon nanotubes, we show that for tube radii below one nanometer, both the filling velocity and the Jurin rise vary nonmonotonically with the tube radius. Strikingly, with fixed chemical surface properties, this leads to confinement-induced reversal of the tube wettability from hydrophilic to hydrophobic for specific values of the radius. By comparing with a model liquid metal, we show that these effects are not specific to water. Using complementary data from slit channels, we then show that they can be described using the disjoining pressure associated with the liquid structuring in confinement. This breakdown of the standard continuum framework is of main importance in the context of capillary effects in nanoporous media, with potential interests ranging from membrane selectivity to mechanical energy storage.
DOI
28
Conserved Amphipathic Helices Mediate Lipid Droplet Targeting of Perilipins 1-3 - Rowe, Emily R. and Mimmack, Michael L. and Barbosa, Antonio D. and Haider, Afreen and Isaac, Iona and Ouberai, Myriam M. and Thiam, Abdou Rachid and Patel, Satish and Saudek, Vladimir and Siniossoglou, Symeon and Savage, David B.
JOURNAL OF BIOLOGICAL CHEMISTRY 2916664-6678 (2016)

Abstract : Perilipins (PLINs) play a key role in energy storage by orchestrating the activity of lipases on the surface of lipid droplets. Failure of this activity results in severe metabolic disease in humans. Unlike all other lipid droplet-associated proteins, PLINs localize almost exclusively to the phospholipid monolayer surrounding the droplet. To understand how they sense and associate with the unique topology of the droplet surface, we studied the localization of human PLINs in Saccharomyces cerevisiae, demonstrating that the targeting mechanism is highly conserved and that 11-mer repeat regions are sufficient for droplet targeting. Mutations designed to disrupt folding of this region into amphipathic helices (AHs) significantly decreased lipid droplet targeting in vivo and in vitro. Finally, we demonstrated a substantial increase in the helicity of this region in the presence of detergent micelles, which was prevented by an AH-disrupting missense mutation. We conclude that highly conserved 11-mer repeat regions of PLINs target lipid droplets by folding into AHs on the droplet surface, thus enabling PLINs to regulate the interface between the hydrophobic lipid core and its surrounding hydrophilic environment.
DOI
29
Snapshot of sequential SNARE assembling states between membranes shows that N-terminal transient assembly initializes fusion - Wang, Yong Jian and Li, Feng and Rodriguez, Nicolas and Lafosse, Xavier and Gourier, Christine and Perez, Eric and Pincet, Frederic
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 1133533-3538 (2016)

Abstract : Many prominent biological processes are driven by protein assembling between membranes. Understanding the mechanisms then entails determining the assembling pathway of the involved proteins. Because the intermediates are by nature transient and located in the intermembrane space, this determination is generally a very difficult, not to say intractable, problem. Here, by designing a setup with sphere/plane geometry, we have been able to freeze one transient state in which the N-terminal domains of SNARE proteins are assembled. A single camera frame is sufficient to obtain the complete probability of this state with the transmembrane distance. We show that it forms when membranes are 20 nm apart and stabilizes by further assembling of the SNAREs at 8 nm. This setup that fixes the intermembrane distance, and thereby the transient states, while optically probing the level of molecular assembly by Forster resonance energy transfer (FRET) can be used to characterize any other transient transmembrane complexes.
DOI
30
Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves - Bar-Sinai, Yohai and Julien, Jean-Daniel and Sharon, Eran and Armon, Shahaf and Nakayama, Naomi and Adda-Bedia, Mokhtar and Boudaoud, Arezki
PLOS COMPUTATIONAL BIOLOGY 12 (2016)

Abstract : Differentiation into well-defined patterns and tissue growth are recognized as key processes in organismal development. However, it is unclear whether patterns are passively, homogeneously dilated by growth or whether they remodel during tissue expansion. Leaf vascular networks are well-fitted to investigate this issue, since leaves are approximately two-dimensional and grow manyfold in size. Here we study experimentally and computationally how vein patterns affect growth. We first model the growing vasculature as a network of viscoelastic rods and consider its response to external mechanical stress. We use the so-called texture tensor to quantify the local network geometry and reveal that growth is heterogeneous, resembling non-affine deformations in composite materials. We then apply mechanical forces to growing leaves after veins have differentiated, which respond by anisotropic growth and reorientation of the network in the direction of external stress. External mechanical stress appears to make growth more homogeneous, in contrast with the model with viscoelastic rods. However, we reconcile the model with experimental data by incorporating randomness in rod thickness and a threshold in the rod growth law, making the rods viscoelastoplastic. Altogether, we show that the higher stiffness of veins leads to their reorientation along external forces, along with a reduction in growth heterogeneity. This process may lead to the reinforcement of leaves against mechanical stress. More generally, our work contributes to a framework whereby growth and patterns are coordinated through the differences in mechanical properties between cell types.
DOI
31
A Programmable DNA Origami Platform to Organize SNAREs for Membrane Fusion - Xu, Weiming and Nathwani, Bhavik and Lin, Chenxiang and Wan, Jing and Karatekin, Erdem and Pincet, Frederic and Shih, William and Rothman, James E.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1384439-4447 (2016)

Abstract : Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes are the core molecular machinery of membrane fusion, a fundamental process that drives inter- and intracellular communication and trafficking. One of the questions that remains controversial has been whether and how SNAREs cooperate. Here we show the use of self-assembled DNA-nanostructure rings to template uniform-sized small unilamellar vesicles containing predetermined maximal number of externally facing SNAREs to study the membrane-fusion process. We also incorporated lipid-conjugated complementary ssDNA as tethers into vesicle and target membranes, which enabled bypass of the rate-limiting docking step of fusion reactions and allowed direct observation of individual membrane-fusion events at SNARE densities as low as one pair per vesicle. With this platform, we confirmed at the single event level that, after docking of the templated-SUVs to supported lipid bilayers (SBL), one to two pairs of SNAREs are sufficient to drive fast lipid mixing. Modularity and programmability of this platform makes it readily amenable to studying more complicated systems where auxiliary proteins are involved.
DOI
32
Scaling Behavior for Ionic Transport and its Fluctuations in Individual Carbon Nanotubes - Secchi, Eleonora and Nigues, Antoine and Jubin, Laetitia and Siria, Alessandro and Bocquet, Lyderic
PHYSICAL REVIEW LETTERS 116 (2016)

Abstract : In this Letter, we perform an experimental study of ionic transport and current fluctuations inside individual carbon nanotubes (CNTs). The conductance exhibits a power law behavior at low salinity, with an exponent close to 1/3 versus the salt concentration in this regime. This behavior is rationalized in terms of a salinity dependent surface charge, which is accounted for on the basis of a model for hydroxide adsorption at the (hydrophobic) carbon surface. This is in contrast to boron nitride nanotubes which exhibit a constant surface conductance. Further, we measure the low frequency noise of the ionic current in CNTs and show that the amplitude of the noise scales with the surface charge, with data collapsing on a master curve for the various studied CNTs at a given pH.
DOI
33
Velocity Condensation for Magnetotactic Bacteria - Rupprecht, Jean-Francois and Waisbord, Nicolas and Ybert, Christophe and Cottin-Bizonne, Cecile and Bocquet, Lyderic
PHYSICAL REVIEW LETTERS 116 (2016)

Abstract : Magnetotactic swimmers tend to align along magnetic field lines against stochastic reorientations. We show that the swimming strategy, e.g., active Brownian motion versus run-and-tumble dynamics, strongly affects the orientation statistics. The latter can exhibit a velocity condensation whereby the alignment probability density diverges. As a consequence, we find that the swimming strategy affects the nature of the phase transition to collective motion, indicating that Levy run-and-tumble walks can outperform active Brownian processes as strategies to trigger collective behavior.
DOI
34
Fluctuations of Electrical Conductivity: A New Source for Astrophysical Magnetic Fields - Petrelis, F. and Alexakis, A. and Gissinger, C.
PHYSICAL REVIEW LETTERS 116 (2016)

Abstract : We consider the generation of a magnetic field by the flow of a fluid for which the electrical conductivity is nonuniform. A new amplification mechanism is found which leads to dynamo action for flows much simpler than those considered so far. In particular, the fluctuations of the electrical conductivity provide a way to bypass antidynamo theorems. For astrophysical objects, we show through three-dimensional global numerical simulations that the temperature-driven fluctuations of the electrical conductivity can amplify an otherwise decaying large scale equatorial dipolar field. This effect could play a role for the generation of the unusually tilted magnetic field of the iced giants Neptune and Uranus.
DOI
35
Acoustic Measurement of Surface Wave Damping by a Meniscus - Michel, Guillaume and Petrelis, Francois and Fauve, Stephan
PHYSICAL REVIEW LETTERS 116 (2016)

Abstract : We investigate the reflection of gravity-capillary surface waves by a plane vertical barrier. The size of the meniscus is found to strongly affect reflection: the energy of the reflected wave with a pinned contact line is around twice the one corresponding to a fully developed meniscus. To perform these measurements, a new experimental setup similar to an acousto-optic modulator is developed and offers a simple way to measure the amplitude, frequency and direction of propagation of surface waves.
DOI
36
The number of accessible paths in the hypercube - Berestycki, Julien and Brunet, Eric and Shi, Zhan
BERNOULLI 22653-680 (2016)

Abstract : Motivated by an evolutionary biology question, we study the following problem: we consider the hypercube \0,1\(L) where each node carries an independent random variable uniformly distributed on [0, 1], except (1, 1,..., 1) which carries the value 1 and (0, 0,..., 0) which carries the value x is an element of [0, 1]. We study the number Theta of paths from vertex (0, 0,, 0) to the opposite vertex (1, 1,..., 1) along which the values on the nodes form an increasing sequence. We show that if the value on (0, 0,..., 0) is set to x = X/L then Theta/L converges in law as L -> infinity to e(-X) times the product of two standard independent exponential variables. As a first step in the analysis, we study the same question when the graph is that of a tree where the root has arity L, each node at level 1 has arity L - 1,..., and the nodes at level L - 1 have only one offspring which are the leaves of the tree (all the leaves are assigned the value 1, the root the value x is an element of [0, 11).
DOI
37
Control of plasma membrane lipid homeostasis by the extended synaptotagmins - Saheki, Yasunori and Bian, Xin and Schauder, Curtis M. and Sawaki, Yujin and Surma, Michal A. and Klose, Christian and Pincet, Frederic and Reinisch, Karin M. and De Camilli, Pietro
NATURE CELL BIOLOGY 18504+ (2016)

Abstract : Acute metabolic changes in plasma membrane (PM) lipids, such as those mediating signalling reactions, are rapidly compensated by homeostatic responses whose molecular basis is poorly understood. Here we show that the extended synaptotagmins (E-Syts), endoplasmic reticulum (ER) proteins that function as PtdIns(4,5)P-2- and Ca2+-regulated tethers to the PM, participate in these responses. E-Syts transfer glycerolipids between bilayers in vitro, and this transfer requires Ca2+ and their lipid-harbouring SMP domain. Genome-edited cells lacking E-Syts do not exhibit abnormalities in the major glycerolipids at rest, but exhibit enhanced and sustained accumulation of PM diacylglycerol following PtdIns(4,5)P-2 hydrolysis by PLC activation, which can be rescued by expression of E-Syt1, but not by mutant E-Syt1 lacking the SMP domain. The formation of E-Syt-dependent ER-PM tethers in response to stimuli that cleave PtdIns(4,5)P-2 and elevate Ca2+ may help reverse accumulation of diacylglycerol in the PM by transferring it to the ER for metabolic recycling.
DOI
38
Recovering Navier-Stokes Equations from Asymptotic Limits of the Boltzmann Gas Mixture Equation - Bianca, Carlo and Dogbe, Christian
COMMUNICATIONS IN THEORETICAL PHYSICS 65553-562 (2016)

Abstract : This paper is devoted to the derivation of macroscopic fluid dynamics from the Boltzmann mesoscopic dynamics of a binary mixture of hard-sphere gas particles. Specifically the hydrodynamics limit is performed by employing different time and space scalings. The paper shows that, depending on the magnitude of the parameters which define the scaling, the macroscopic quantities (number density, mean velocity and local temperature) are solutions of the acoustic equation, the linear incompressible Euler equation and the incompressible Navier Stokes equation. The derivation is formally tackled by the recent moment method proposed by [C. Bardos, et al., J. Stat. Phys. 63 (1991) 323] and the results generalize the analysis performed in [C. Bianca, et al., Commun. Nonlinear Sci. Numer. Simulat. 29 (2015) 240].
DOI
39
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models - Jacquin, Hugo and Gilson, Amy and Shakhnovich, Eugene and Cocco, Simona and Monasson, Remi
PLOS COMPUTATIONAL BIOLOGY 12 (2016)

Abstract : Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use lattice protein model (LP) to benchmark those inverse statistical approaches. We build MSA of highly stable sequences in target LP structures, and infer the effective pairwise Potts Hamiltonians from those MSA. We find that inferred Potts Hamiltonians reproduce many important aspects of `true' LP structures and energetics. Careful analysis reveals that effective pairwise couplings in inferred Potts Hamiltonians depend not only on the energetics of the native structure but also on competing folds; in particular, the coupling values reflect both positive design (stabilization of native conformation) and negative design (destabilization of competing folds). In addition to providing detailed structural information, the inferred Potts models used as protein Hamiltonian for design of new sequences are able to generate with high probability completely new sequences with the desired folds, which is not possible using independent-site models. Those are remarkable results as the effective LP Hamiltonians used to generate MSA are not simple pairwise models due to the competition between the folds. Our findings elucidate the reasons for the success of inverse approaches to the modelling of proteins from sequence data, and their limitations.
DOI
40
Defects at the Nanoscale Impact Contact Line Motion at all Scales - Perrin, Hugo and Lhermerout, Romain and Davitt, Kristina and Rolley, Etienne and Andreotti, Bruno
PHYSICAL REVIEW LETTERS 116 (2016)

Abstract : The contact angle of a liquid drop moving on a real solid surface depends on the speed and direction of motion of the three-phase contact line. Many experiments have demonstrated that pinning on surface defects, thermal activation and viscous dissipation impact contact line dynamics, but so far, efforts have failed to disentangle the role of each of these dissipation channels. Here, we propose a unifying multiscale approach that provides a single quantitative framework. We use this approach to successfully account for the dynamics measured in a classic dip-coating experiment performed over an unprecedentedly wide range of velocity. We show that the full contact line dynamics up to the liquid film entrainment threshold can be parametrized by the size, amplitude and density of nanometer-scale defects. This leads us to reinterpret the contact angle hysteresis as a dynamical crossover rather than a depinning transition.