laboratoire de physique statistique
laboratoire de physique statistique


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.
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
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.
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

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.
Activated desorption at heterogeneous interfaces and long-time kinetics of hydrocarbon recovery from nanoporous media - Lee, Thomas and Bocquet, Lyderic and Coasne, Benoit

Abstract : Hydrocarbon recovery from unconventional reservoirs (shale gas) is debated due to its environmental impact and uncertainties on its predictability. But a lack of scientific knowledge impedes the proposal of reliable alternatives. The requirement of hydrofracking, fast recovery decay and ultra-low permeability-inherent to their nanoporosity-are specificities of these reservoirs, which challenge existing frameworks. Here we use molecular simulation and statistical models to show that recovery is hampered by interfacial effects at the wet kerogen surface. Recovery is shown to be thermally activated with an energy barrier modelled from the interface wetting properties. We build a statistical model of the recovery kinetics with a two-regime decline that is consistent with published data: a short time decay, consistent with Darcy description, followed by a fast algebraic decay resulting from increasingly unreachable energy barriers. Replacing water by CO2 or propane eliminates the barriers, therefore raising hopes for clean/efficient recovery.
A moving contact line as a rheometer for nanometric interfacial layers - Lhermerout, Romain and Perrin, Hugo and Rolley, Etienne and Andreotti, Bruno and Davitt, Kristina

Abstract : How a liquid drop sits or moves depends on the physical and mechanical properties of the underlying substrate. This can be seen in the hysteresis of the contact angle made by a drop on a solid, which is known to originate from surface heterogeneities, and in the slowing of droplet motion on deformable solids. Here, we show how a moving contact line can be used to characterize a molecularly thin polymer layer on a solid. We find that the hysteresis depends on the polymerization index and can be optimized to be vanishingly small (< 0.07 degrees). The mechanical properties are quantitatively deduced from the microscopic contact angle, which is proportional to the speed of the contact line and the Rouse relaxation time divided by the layer thickness, in agreement with theory. Our work opens the prospect of measuring the properties of functionalized interfaces in microfluidic and biomedical applications that are otherwise inaccessible.
Massive radius-dependent flow slippage in carbon nanotubes - Secchi, Eleonora and Marbach, Sophie and Nigues, Antoine and Stein, Derek and Siria, Alessandro and Bocquet, Lyderic
NATURE 537210-213 (2016)

Abstract : Measurements and simulations have found that water moves through carbon nanotubes at exceptionally high rates owing to nearly frictionless interfaces(1-4). These observations have stimulated interest in nanotube-based membranes for applications including desalination, nano-filtration and energy harvesting(5-10), yet the exact mechanisms of water transport inside the nanotubes and at the water-carbon interface continue to be debated(11,12) because existing theories do not provide a satisfactory explanation for the limited number of experimental results available so far(13). This lack of experimental results arises because, even though controlled and systematic studies have explored transport through individual nanotubes(7-9,14-17), none has met the considerable technical challenge of unambiguously measuring the permeability of a single nanotube(11). Here we show that the pressure-driven flow rate through individual nanotubes can be determined with unprecedented sensitivity and without dyes from the hydrodynamics of water jets as they emerge from single nanotubes into a surrounding fluid. Our measurements reveal unexpectedly large and radius-dependent surface slippage in carbon nanotubes, and no slippage in boron nitride nanotubes that are crystallographically similar to carbon nanotubes, but electronically different. This pronounced contrast between the two systems must originate from subtle differences in the atomic-scale details of their solid-liquid interfaces, illustrating that nanofluidics is the frontier at which the continuum picture of fluid mechanics meets the atomic nature of matter.
Local equilibrium in bird flocks - Mora, Thierry and Walczak, Aleksandra M. and Del Castello, Lorenzo and Ginelli, Francesco and Melillo, Stefania and Parisi, Leonardo and Viale, Massimiliano and Cavagna, Andrea and Giardina, Irene
Nature Physics 121153+ (2016)

Abstract : The correlated motion of flocks is an example of global order emerging from local interactions. An essential difference with respect to analogous ferromagnetic systems is that flocks are active: animals move relative to each other, dynamically rearranging their interaction network. This non-equilibrium characteristic has been studied theoretically, but its impact on actual animal groups remains to be fully explored experimentally. Here, we introduce a novel dynamical inference technique, based on the principle of maximum entropy, which accommodates network rearrangements and overcomes the problem of slow experimental sampling rates. We use this method to infer the strength and range of alignment forces from data of starling flocks. We find that local bird alignment occurs on a much faster timescale than neighbour rearrangement. Accordingly, equilibrium inference, which assumes a fixed interaction network, gives results consistent with dynamical inference. We conclude that bird orientations are in a state of local quasi-equilibrium over the interaction length scale, providing firm ground for the applicability of statistical physics in certain active systems.
Breakdown of elasticity in amorphous solids - Biroli, Giulio and Urbani, Pierfrancesco
Nature Physics 121130-1133 (2016)

Abstract : What characterizes a solid is the way that it responds to external stresses. Ordered solids, such as crystals, exhibit an elastic regime followed by a plastic regime, both understood microscopically in terms of lattice distortion and dislocations. For amorphous solids the situation is instead less clear, and the microscopic understanding of the response to deformation and stress is a very active research topic. Several studies have revealed that even in the elastic regime the response is very jerky at low temperature, resembling very much the response of disordered magnetic materials(1-6). Here we show that in a very large class of amorphous solids this behaviour emerges upon decreasing temperature, as a phase transition, where standard elastic behaviour breaks down. At the transition all nonlinear elastic moduli diverge and standard elasticity theory no longer holds. Below the transition, the response to deformation becomes history- and time-dependent.
In vitro transport activity of the fully assembled MexAB-OprM efflux pump from Pseudomonas aeruginosa - Verchere, Alice and Dezi, Manuela and Adrien, Vladimir and Broutin, Isabelle and Picard, Martin

Abstract : Antibiotic resistance is a major public health issue and many bacteria responsible for human infections have now developed a variety of antibiotic resistance mechanisms. For instance, Pseudomonas aeruginosa, a disease-causing Gram-negative bacteria, is now resistant to almost every class of antibiotics. Much of this resistance is attributable to multidrug efflux pumps, which are tripartite membrane protein complexes that span both membranes and actively expel antibiotics. Here we report an in vitro procedure to monitor transport by the tripartite MexAB-OprM pump. By combining proteoliposomes containing the MexAB and OprM portions of the complex, we are able to assay energy-dependent substrate translocation in a system that mimics the dual-membrane architecture of Gram-negative bacteria. This assay facilitates the study of pump transport dynamics and could be used to screen pump inhibitors with potential clinical use in restoring therapeutic activity of old antibiotics.
Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities - Fiorini, Francesca and Bagchi, Debjani and Le Hir, Herve and Croquette, Vincent

Abstract : RNA helicases are implicated in most cellular RNA-dependent events. In eukaryotes however, only few have been functionally characterized. Upf1 is a RNA helicase essential for nonsense-mediated mRNA decay (NMD). Here, using magnetic tweezers and bulk assays, we observe that human Upf1 is able to translocate slowly over long single-stranded nucleic acids with a processivity >10 kb. Upf1 efficiently translocates through double-stranded structures and protein-bound sequences, demonstrating that Upf1 is an efficient ribonucleoprotein complex remodeler. Our observation of processive unwinding by an eukaryotic RNA helicase reveals that Upf1, once recruited onto NMD mRNA targets, can scan the entire transcript to irreversibly remodel the mRNP, facilitating its degradation by the NMD machinery.
Phonon modes for faster flow - Bocquet, Lyderic and Netz, Roland R.
Dynamical backaction cooling with free electrons - Nigues, A. and Siria, A. and Verlot, P.

Abstract : The ability to cool single ions, atomic ensembles, and more recently macroscopic degrees of freedom down to the quantum ground state has generated considerable progress and perspectives in fundamental and technological science. These major advances have been essentially obtained by coupling mechanical motion to a resonant electromagnetic degree of freedom in what is generally known as laser cooling. Here, we experimentally demonstrate the first self-induced coherent cooling mechanism that is not mediated by an electromagnetic resonance. Using a focused electron beam, we report a 50-fold reduction of the motional temperature of a nanowire. Our result primarily relies on the sub-nanometre confinement of the electron beam and generalizes to any delayed and spatially confined interaction, with important consequences for near-field microscopy and fundamental nanoscale dissipation mechanisms.
Efimov-driven phase transitions of the unitary Bose gas - Piatecki, Swann and Krauth, Werner

Abstract : Initially predicted in nuclear physics, Efimov trimers are bound configurations of three quantum particles that fall apart when any one of them is removed. They open a window into a rich quantum world that has become the focus of intense experimental and theoretical research, as the region of `unitary' interactions, where Efimov trimers form, is now accessible in cold-atom experiments. Here we use a path-integral Monte Carlo algorithm backed up by theoretical arguments to show that unitary bosons undergo a first-order phase transition from a normal gas to a superfluid Efimov liquid, bound by the same effects as Efimov trimers. A triple point separates these two phases and another superfluid phase, the conventional Bose-Einstein condensate, whose coexistence line with the Efimov liquid ends in a critical point. We discuss the prospects of observing the proposed phase transitions in cold-atom systems.
Emergence of collective modes and tri-dimensional structures from epithelial confinement - Deforet, M. and Hakim, V. and Yevick, H. G. and Duclos, G. and Silberzan, P.

Abstract : Many in vivo processes, including morphogenesis or tumour maturation, involve small populations of cells within a spatially restricted region. However, the basic mechanisms underlying the dynamics of confined cell assemblies remain largely to be deciphered and would greatly benefit from well-controlled in vitro experiments. Here we show that confluent epithelial cells cultured on finite population-sized domains, exhibit collective low-frequency radial displacement modes as well as stochastic global rotation reversals. A simple mathematical model, in which cells are described as persistent random walkers that adapt their motion to that of their neighbours, captures the essential characteristics of these breathing oscillations. As these epithelia mature, a tri-dimensional peripheral cell cord develops at the domain edge by differential extrusion, as a result of the additional degrees of freedom of the border cells. These results demonstrate that epithelial confinement alone can induce morphogenesis-like processes including spontaneous collective pulsations and transition from 2D to 3D.
Rods in daylight act as relay cells for cone-driven horizontal cell mediated surround inhibition - Szikra, Tamas and Trenholm, Stuart and Drinnenberg, Antonia and Juettner, Josephine and Raics, Zoltan and Farrow, Karl and Biel, Martin and Awatramani, Gautam and Clark, Damon A. and Sahel, Jose-Alain and da Silveira, Rava Azeredo and Roska, Botond
NATURE NEUROSCIENCE 171728-1735 (2014)

Abstract : Vertebrate vision relies on two types of photoreceptors, rods and cones, which signal increments in light intensity with graded hyperpolarizations. Rods operate in the lower range of light intensities while cones operate at brighter intensities. The receptive fields of both photoreceptors exhibit antagonistic center-surround organization. Here we show that at bright light levels, mouse rods act as relay cells for cone-driven horizontal cell-mediated surround inhibition. In response to large, bright stimuli that activate their surrounds, rods depolarize. Rod depolarization increases with stimulus size, and its action spectrum matches that of cones. Rod responses at high light levels are abolished in mice with nonfunctional cones and when horizontal cells are reversibly inactivated. Rod depolarization is conveyed to the inner retina via postsynaptic circuit elements, namely the rod bipolar cells. Our results show that the retinal circuitry repurposes rods, when they are not directly sensing light, to relay cone-driven surround inhibition.
Controlling coherence via tuning of the population imbalance in a bipartite optical lattice - Di Liberto, M. and Comparin, T. and Kock, T. and Oelschlaeger, M. and Hemmerich, A. and Smith, C. Morais

Abstract : The control of transport properties is a key tool at the basis of many technologically relevant effects in condensed matter. The clean and precisely controlled environment of ultracold atoms in optical lattices allows one to prepare simplified but instructive models, which can help to better understand the underlying physical mechanisms. Here we show that by tuning a structural deformation of the unit cell in a bipartite optical lattice, one can induce a phase transition from a superfluid into various Mott insulating phases forming a shell structure in the superimposed harmonic trap. The Mott shells are identified via characteristic features in the visibility of Bragg maxima in momentum spectra. The experimental findings are explained by Gutzwiller mean-field and quantum Monte Carlo calculations. Our system bears similarities with the loss of coherence in cuprate superconductors, known to be associated with the doping-induced buckling of the oxygen octahedra surrounding the copper sites.
Preparation and characterization of SNARE-containing nanodiscs and direct study of cargo release through fusion pores - Shi, Lei and Howan, Kevin and Shen, Qing-Tao and Wang, Yong Jian and Rothman, James E. and Pincet, Frederic
NATURE PROTOCOLS 8935-948 (2013)

Abstract : This protocol describes an assay that uses suspended nanomembranes called nanodiscs to analyze fusion events. A nanodisc is a lipid bilayer wrapped by membrane scaffold proteins. Fluorescent lipids and a protein that is part of a fusion machinery, VAMP2 in the example detailed herein, are included in the nanodiscs. Upon fusion of a nanodisc with a nonfluorescent liposome containing cognate proteins (for instance, the VAMP2 cognate syntaxin1/SNAP-25 complex), the fluorescent lipids are dispersed in the liposome and the increase in fluorescence, initially quenched in the nanodisc, is monitored on a plate reader. Because the scaffold proteins restrain pore expansion, the fusion pore eventually reseals. A reducing agent, such as dithionite, which can quench the fluorescence of accessible lipids, can then be used to determine the number of fusion events. A fluorescence-based approach can also be used to monitor the release of encapsulated cargo. From data on the total cargo release and the number of the much faster lipid- mixing events, the researcher may determine the amount of cargo released per fusion event. This assay requires 3 d for preparation and 4 h for data acquisition and analysis.
RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue - Manosas, Maria and Perumal, Senthil K. and Bianco, Piero and Ritort, Felix and Benkovic, Stephen J. and Croquette, Vincent

Abstract : Helicases that both unwind and rewind DNA have central roles in DNA repair and genetic recombination. In contrast to unwinding, DNA rewinding by helicases has proved difficult to characterize biochemically because of its thermodynamically downhill nature. Here we use single-molecule assays to mechanically destabilize a DNA molecule and follow, in real time, unwinding and rewinding by two DNA repair helicases, bacteriophage T4 UvsW and Escherichia coli RecG. We find that both enzymes are robust rewinding enzymes, which can work against opposing forces as large as 35 pN, revealing their active character. The generation of work during the rewinding reaction allows them to couple rewinding to DNA unwinding and/or protein displacement reactions central to the rescue of stalled DNA replication forks. The overall results support a general mechanism for monomeric rewinding enzymes.
The biophysics and cell biology of lipid droplets - Thiam, Abdou Rachid and Farese, Jr., Robert V. and Walther, Tobias C.

Abstract : Lipid droplets are intracellular organelles that are found in most cells, where they have fundamental roles in metabolism. They function prominently in storing oil-based reserves of metabolic energy and components of membrane lipids. Lipid droplets are the dispersed phase of an oil-in-water emulsion in the aqueous cytosol of cells, and the importance of basic biophysical principles of emulsions for lipid droplet biology is now being appreciated. Because of their unique architecture, with an interface between the dispersed oil phase and the aqueous cytosol, specific mechanisms underlie their formation, growth and shrinkage. Such mechanisms enable cells to use emulsified oil when the demands for metabolic energy or membrane synthesis change. The regulation of the composition of the phospholipid surfactants at the surface of lipid droplets is crucial for lipid droplet homeostasis and protein targeting to their surfaces.