laboratoire de physique statistique
 
 
laboratoire de physique statistique

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2014
Log-periodic Critical Amplitudes: A Perturbative Approach - Derrida, Bernard and Giacomin, Giambattista
JOURNAL OF STATISTICAL PHYSICS 154286-304 (2014)

Abstract : Log-periodic amplitudes appear in the critical behavior of a large class of systems, in particular when a discrete scale invariance is present. Here we show how to compute these critical amplitudes perturbatively when they originate from a renormalization map which is close to a monomial. In this case, the log-periodic amplitudes of the subdominant corrections to the leading critical behavior can also be calculated.
Comparing open and closed molecular self-assembly - Castelnovo, M. and Verdier, T. and Foret, L.
EPL 105 (2014)

Abstract : We study theoretically in the present work the self-assembly of molecules in an open system, which is fed by monomers and depleted in partial or complete clusters. Such a scenario is likely to occur for example in the context of viral self-assembly. We provide a general formula for the mean-field size distribution which is valid both at equilibrium in a closed system, and in the stationary state in an open system. This allows us to explore in a simple way out-of-equilibrium features for self-assembly and compare them to equilibrium properties. In particular, we identify a region of parameter space for which the out-of-equilibrium size distribution in the presence of external fluxes is equal to the equilibrium size distribution in the absence of external fluxes, up to a constant renormalization factor. The range of validity of this result and its consequences are discussed. Copyright (c) EPLA, 2014
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems - Sterpone, Fabio and Melchionna, Simone and Tuffery, Pierre and Pasquali, Samuela and Mousseau, Normand and Cragnolini, Tristan and Chebaro, Yassmine and St-Pierre, Jean-Francois and Kalimeri, Maria and Barducci, Alessandro and Laurin, Yoann and Tek, Alex and Baaden, Marc and Phuong Hoang Nguyen and Derreumaux, Philippe
CHEMICAL SOCIETY REVIEWS 434871-4893 (2014)

Abstract : The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation - Rouault, Herve and Santolini, Marc and Schweisguth, Francois and Hakim, Vincent
NUCLEIC ACIDS RESEARCH 426128-6145 (2014)

Abstract : Cis-regulatory modules (CRMs) and motifs play a central role in tissue and condition-specific gene expression. Here we present Imogene, an ensemble of statistical tools that we have developed to facilitate their identification and implemented in a publicly available software. Starting from a small training set of mammalian or fly CRMs that drive similar gene expression profiles, Imogene determines de novo cis-regulatory motifs that underlie this co-expression. It can then predict on a genome-wide scale other CRMs with a regulatory potential similar to the training set. Imogene bypasses the need of large datasets for statistical analyses by making central use of the information provided by the sequenced genomes of multiple species, based on the developed statistical tools and explicit models for transcription factor binding site evolution. We test Imogene on characterized tissue-specific mouse developmental CRMs. Its ability to identify CRMs with the same specificity based on its de novo created motifs is comparable to that of previously evaluated `motif-blind' methods. We further show, both in flies and in mammals, that Imogene de novo generated motifs are sufficient to discriminate CRMs related to different developmental programs. Notably, purely relying on sequence data, Imogene performs as well in this discrimination task as a previously reported learning algorithm based on Chromatin Immunoprecipitation (ChIP) data for multiple transcription factors at multiple developmental stages.
Single-step microfluidic fabrication of soft monodisperse polyelectrolyte microcapsules by interfacial complexation - Kaufman, Gilad and Boltyanskiy, Rostislav and Nejati, Siamak and Thiam, Abdou R. and Loewenberg, Michael and Dufresne, Eric R. and Osuji, Chinedum O.
LAB ON A CHIP 143494-3497 (2014)

Abstract : Common methods for fabrication of polyelectrolyte microcapsules rely on a multi-step process. We propose a single-step approach to generate polyelectrolyte microcapsules with 1-2 m shells based on polyelectrolyte complexation across a water/oil droplet interface and study the effect of parameters controlling the polyelectrolyte complexation on shell thickness.
Morphology of melanocytic lesions in situ - Balois, Thibaut and Ben Amar, Martine
SCIENTIFIC REPORTS 4 (2014)

Abstract : Melanoma is a solid tumour with its own specificity from the biological and morphological viewpoint. On one hand, numerous mutations are already known affecting different pathways. They usually concern proliferation rate, apoptosis, cell senescence and cell behaviour. On the other hand, several visual criteria at the tissue level are used by physicians in order to diagnose skin lesions. Nevertheless, the mechanisms between the changes from the mutations at the cell level to the morphology exhibited at the tissue level are still not fully understood. Using physical tools, we develop a simple model. We demonstrate analytically that it contains the necessary ingredients to understand several specificities of melanoma such as the presence of microstructures inside a skin lesion or the absence of a necrotic core. We also explain the importance of senescence for growth arrest in benign skin lesions. Thanks to numerical simulations, we successfully compare this model to biological data.
Dislocation networks in He-4 crystals - Fefferman, A. D. and Souris, F. and Haziot, A. and Beamish, J. R. and Balibar, S.
PHYSICAL REVIEW B 89 (2014)

Abstract : The mechanical behavior of crystals is dominated by dislocation networks, their structure, and their interactions with impurities or thermal phonons. However, in classical crystals, networks are usually random with impurities often forming nonequilibrium clusters when their motion freezes at low temperature. Helium provides unique advantages for the study of dislocations: Crystals are free of all but isotopic impurities, the concentration of these can be reduced to the parts per 10(9) (ppb) level, and the impurities are mobile at all temperatures and therefore remain in equilibrium with the dislocations. We have achieved a comprehensive study of the mechanical response of He-4 crystals to a driving strain as a function of temperature, frequency, and strain amplitude. The quality of our fits to the complete set of data strongly supports our assumption of stringlike vibrating dislocations. It leads to a precise determination of the distribution of dislocation network lengths and to detailed information about the interaction between dislocations and both thermal phonons and He-3 impurities. The width of the dissipation peak associated with impurity binding is larger than predicted by a simple Debye model, and much of this broadening is due to the distribution of network lengths.
Reconstruction and Identification of DNA Sequence Landscapes from Unzipping Experiments at Equilibrium - Barbieri, Carlo and Cocco, Simona and Jorg, Thomas and Monasson, Remi
BIOPHYSICAL JOURNAL 106430-439 (2014)

Abstract : Two methods for reconstructing the free-energy landscape of a DNA molecule from the knowledge of the equilibrium unzipping force versus extension signal are introduced: a simple and fast procedure, based on a parametric representation of the experimental force signal, and a maximum-likelihood inference of coarse-grained free-energy parameters. In addition, we propose a force alignment procedure to correct for the drift in the experimental measure of the opening position, a major source of error. For unzipping data obtained by Huguet et al., the reconstructed basepair (bp) free energies agree with the running average of the true free energies on a 20-50 bp scale, depending on the region in the sequence. Features of the landscape at a smaller scale (5-10 bp) could be recovered in favorable regions at the beginning of the molecule. Based on the analysis of synthetic data corresponding to the 16S rDNA gene of bacteria, we show that our approach could be used to identify specific DNA sequences among thousands of homologous sequences in a database.
Tuning the ordered states of folded rods by isotropic confinement - Bayart, E. and Boudaoud, A. and Adda-Bedia, M.
PHYSICAL REVIEW E 89 (2014)

Abstract : The packing of elastic objects is increasingly studied in the framework of out-of-equilibrium statistical mechanics and thus these appear to be similar to glassy systems. Here, we present a two-dimensional experiment whereby a rod is confined by a parabolic potential. The setup enables spanning a wide range of folded configurations of the rod. Measurements of the distributions of length and curvature in the system reveal the importance of a stacking process whereby many layers of the rod are grouped into branches. The geometrical order of patterns increases with the confinement strength. Measurements of the distributions of energies lead to the definition of an energy scale that is correlated with the elastic energy of the stacked parts of the rod. This scale imposes energy partition in the system and might be relevant to the framework of the thermodynamics of disordered systems. Following these observations, we describe the patterns as excited states of a ground state corresponding to the most ordered geometry. Eventually, we provide evidence that the disordered state of a folded rod becomes spontaneously closer to the ground state as confinement is increased.
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Correlated Lateral Diffusion of Lipids - Adrien, Vladimir and Rayan, Gamal and Taulier, Nicolas and Urbach, Wladimir
BIOPHYSICAL JOURNAL 10684A (2014)
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11
Optical signatures of a fully dark exciton condensate - Combescot, Monique and Combescot, Roland and Alloing, Mathieu and Dubin, Francois
EPL 105 (2014)

Abstract : We propose optical means to reveal the presence of a dark exciton condensate that does not yield any photoluminescence at all. We show that i) the dark exciton density can be obtained from the blueshift of the excitonic absorption line induced by dark excitons; ii) the polarization of the dark condensate can be obtained from the blueshift dependence on the probe photon polarization as well as from the Faraday effect. All these effects result from carrier exchanges between dark and bright states. Copyright (C) EPLA, 2014
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12
Arf1/COPI machinery acts directly on lipid droplets and enables their connection to the ER for protein targeting - Wilfling, Florian and Thiam, Abdou Rachid and Olarte, Maria-Jesus and Wang, Jing and Beck, Rainer and Gould, Travis J. and Allgeyer, Edward S. and Pincet, Frederic and Bewersdorf, Joerg and Farese, Jr., Robert V. and Walther, Tobias C.
ELIFE 3 (2014)

Abstract : Lipid droplets (LDs) are ubiquitous organelles that store neutral lipids, such as triacylglycerol (TG), as reservoirs of metabolic energy and membrane precursors. The Arf1/COPI protein machinery, known for its role in vesicle trafficking, regulates LD morphology, targeting of specific proteins to LDs and lipolysis through unclear mechanisms. Recent evidence shows that Arf1/COPI can bud nano-LDs (similar to 60 nm diameter) from phospholipid-covered oil/water interfaces in vitro. We show that Arf1/COPI proteins localize to cellular LDs, are sufficient to bud nano-LDs from cellular LDs, and are required for targeting specific TG-synthesis enzymes to LD surfaces. Cells lacking Arf1/COPI function have increased amounts of phospholipids on LDs, resulting in decreased LD surface tension and impairment to form bridges to the ER. Our findings uncover a function for Arf1/COPI proteins at LDs and suggest a model in which Arf1/COPI machinery acts to control ER-LD connections for localization of key enzymes of TG storage and catabolism.
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13
Generalized event-chain Monte Carlo: Constructing rejection-free global-balance algorithms from infinitesimal steps - Michel, Manon and Kapfer, Sebastian C. and Krauth, Werner
JOURNAL OF CHEMICAL PHYSICS 140 (2014)

Abstract : In this article, we present an event-driven algorithm that generalizes the recent hard-sphere event-chain Monte Carlo method without introducing discretizations in time or in space. A factorization of the Metropolis filter and the concept of infinitesimal Monte Carlo moves are used to design a rejection-free Markov-chain Monte Carlo algorithm for particle systems with arbitrary pairwise interactions. The algorithm breaks detailed balance, but satisfies maximal global balance and performs better than the classic, local Metropolis algorithm in large systems. The new algorithm generates a continuum of samples of the stationary probability density. This allows us to compute the pressure and stress tensor as a byproduct of the simulation without any additional computations. (C) 2014 AIP Publishing LLC.
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14
Diagrammatic Monte Carlo study of the Fermi polaron in two dimensions - Vlietinck, Jonas and Ryckebusch, Jan and Van Houcke, Kris
PHYSICAL REVIEW B 89 (2014)

Abstract : We study the properties of the two-dimensional Fermi polaron model in which an impurity attractively interacts with a Fermi sea of particles in the zero-range limit. We use a diagrammatic Monte Carlo (DiagMC) method which allows us to sample a Feynman diagrammatic series to very high order. The convergence properties of the series and the role of multiple particle-hole excitations are discussed. We study the polaron and molecule energy as a function of the coupling strength, revealing a transition from a polaron to a molecule in the ground state. We find a value for the critical interaction strength which complies with the experimentally measured one and predictions from variational methods. For all considered interaction strengths, the polaron Z factor from the full diagrammatic series almost coincides with the one-particle-hole result. We also formally link the DiagMC and the variational approaches for the polaron problem at hand.
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15
Quantum walks in artificial electric and gravitational fields - Di Molfetta, Giuseppe and Brachet, Marc and Debbasch, Fabrice
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 397157-168 (2014)

Abstract : The continuous limit of quantum walks (QWs) on the line is revisited through a new, recently developed method. In all cases but one, the limit coincides with the dynamics of a Dirac fermion coupled to an artificial electric and/or relativistic gravitational field. All results are carefully discussed and illustrated by numerical simulations. Possible experimental realizations are also addressed. (C) 2013 Elsevier B.V. All rights reserved.
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16
Efimov-driven phase transitions of the unitary Bose gas - Piatecki, Swann and Krauth, Werner
NATURE COMMUNICATIONS 5 (2014)

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.
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17
A Half-Zippered SNARE Complex Represents a Functional Intermediate in Membrane Fusion - Li, Feng and Kuemmel, Daniel and Coleman, Jeff and Reinisch, Karin M. and Rothman, James E. and Pincet, Frederic
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1363456-3464 (2014)

Abstract : SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins mediate fusion by pulling biological membranes together via a zippering mechanism. Recent biophysical studies have shown that t- and v-SNAREs can assemble in multiple stages from the N-termini toward the C-termini. Here we show that functionally, membrane fusion requires a sequential, two-step folding pathway and assign specific and distinct functions for each step. First, the N-terminal domain (NTD) of the v-SNARE docks to the t-SNARE, which leads to a conformational rearrangement into an activated half-zippered SNARE complex. This partially assembled SNARE complex locks the C-terminal (CTD) portion of the t-SNARE into the same structure as in the postfusion 4-helix bundle, thereby creating the binding site for the CTD of the v-SNARE and enabling fusion. Then zippering of the remaining CTD, the membrane-proximal linker (LD), and transmembrane (TMD) domains is required and sufficient to trigger fusion. This intrinsic property of the SNAREs fits well with the action of physiologically vital regulators such as complexin. We also report that NTD assembly is the rate-limiting step. Our findings provide a refined framework for delineating the molecular mechanism of SNARE-mediated membrane fusion and action of regulatory proteins.
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18
Modeling quantum fluid dynamics at nonzero temperatures - Berloff, Natalia G. and Brachet, Marc and Proukakis, Nick P.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 1114675-4682 (2014)

Abstract : The detailed understanding of the intricate dynamics of quantum fluids, in particular in the rapidly growing subfield of quantum turbulence which elucidates the evolution of a vortex tangle in a superfluid, requires an in-depth understanding of the role of finite temperature in such systems. The Landau two-fluidmodel is the most successful hydrodynamical theory of superfluid helium, but by the nature of the scale separations it cannot give an adequate description of the processes involving vortex dynamics and interactions. In our contribution we introduce a framework based on a nonlinear classical-field equation that is mathematically identical to the Landau model and provides a mechanism for severing and coalescence of vortex lines, so that the questions related to the behavior of quantized vortices can be addressed self-consistently. The correct equation of state as well as nonlocality of interactions that leads to the existence of the roton minimum can also be introduced in such description. We review and apply the ideas developed for finite-temperature description of weakly interacting Bose gases as possible extensions and numerical refinements of the proposed method. We apply this method to elucidate the behavior of the vortices during expansion and contraction following the change in applied pressure. We show that at low temperatures, during the contraction of the vortex core as the negative pressure grows back to positive values, the vortex line density grows through a mechanism of vortex multiplication. This mechanism is suppressed at high temperatures.
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19
Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses - Greenbaum, Benjamin D. and Cocco, Simona and Levine, Arnold J. and Monasson, Remi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 1115054-5059 (2014)

Abstract : We outline a theory to quantify the interplay of entropic and selective forces on nucleotide organization and apply it to the genomes of single-stranded RNA viruses. We quantify these forces as intensive variables that can easily be compared between sequences, outline a computationally efficient transfer-matrix method for their calculation, and apply this method to influenza and HIV viruses. We find viruses altering their dinucleotide motif use under selective forces, with these forces on CpG dinucleotides growing stronger in influenza the longer it replicates in humans. For a subset of genes in the human genome, many involved in antiviral innate immunity, the forces acting on CpG dinucleotides are even greater than the forces observed in viruses, suggesting that both effects are in response to similar selective forces involving the innate immune system. We further find that the dynamics of entropic forces balancing selective forces can be used to predict how long it will take a virus to adapt to a new host, and that it would take H1N1 several centuries to adapt to humans from birds, typically contributing many of its synonymous substitutions to the forcible removal of CpG dinucleotides. By examining the probability landscape of dinucleotide motifs, we predict where motifs are likely to appear using only a single-force parameter and uncover the localization of UpU motifs in HIV. Essentially, we extend the natural language and concepts of statistical physics, such as entropy and conjugated forces, to understanding viral sequences and, more generally, constrained genome evolution.
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20
Single neuron dynamics and computation - Brunel, Nicolas and Hakim, Vincent and Richardson, Magnus J. E.
CURRENT OPINION IN NEUROBIOLOGY 25149-155 (2014)

Abstract : At the single neuron level, information processing involves the transformation of input spike trains into an appropriate output spike train. Building upon the classical view of a neuron as a threshold device, models have been developed in recent years that take into account the diverse electrophysiological make-up of neurons and accurately describe their input-output relations. Here, we review these recent advances and survey the computational roles that they have uncovered for various electrophysiological properties, for dendritic arbor anatomy as well as for short-term synaptic plasticity.