laboratoire de physique statistique
 
 
laboratoire de physique statistique

Publications

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BIOPHYSICAL JOURNAL 


21
P U B L I C A T I O N S



 
2016
1
Experimental Measurement of the Activation Energy of Phospholipid Membrane Fusion - Francois-Martin, Claire and Rothman, James E. and Pincet, Frederic
BIOPHYSICAL JOURNAL 110520A (2016)
2
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
BIOPHYSICAL JOURNAL 110370A (2016)
3
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
BIOPHYSICAL JOURNAL 110183A (2016)
4
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
BIOPHYSICAL JOURNAL 11049A-50A (2016)
5
Remodeling of Gamete Membrane during Mammalian Fertilization - Ravaux, Benjamin and Gourier, Christine
BIOPHYSICAL JOURNAL 11018A (2016)
 
2015
6
Protein and RNA Structure Prediction by Integration of Co-Evolutionary Information into Molecular Simulation - De Leonardis, Eleonora and Lutz, Benjamin and Cocco, Simona and Monasson, Remi and Szurmant, Hendrik and Weigt, Martin and Schug, Alexander
BIOPHYSICAL JOURNAL 10813A-14A (2015)
From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets - Murisic, Nebojsa and Hakim, Vincent and Kevrekidis, Ioannis G. and Shvartsman, Stanislav Y. and Audoly, Basile
BIOPHYSICAL JOURNAL 109154-163 (2015)

Abstract : Epithelial tissue, in which cells adhere tightly to each other and to the underlying substrate, is one of the four major tissue types in adult organisms. In embryos, epithelial sheets serve as versatile substrates during the formation of developing organs. Some aspects of epithelial morphogenesis can be adequately described using vertex models, in which the two-dimensional arrangement of epithelial cells is approximated by a polygonal lattice with an energy that has contributions reflecting the properties of individual cells and their interactions. Previous studies with such models have largely focused on dynamics confined to two spatial dimensions and analyzed them numerically. We show how these models can be extended to account for three-dimensional deformations and studied analytically. Starting from the extended model, we derive a continuum plate description of cell sheets, in which the effective tissue properties, such as bending rigidity, are related explicitly to the parameters of the vertex model. To derive the continuum plate model, we duly take into account a microscopic shift between the two sub-lattices of the hexagonal network, which has been ignored in previous work. As an application of the continuum model, we analyze tissue buckling by a line tension applied along a circular contour, a simplified set-up relevant to several situations in the developmental contexts. The buckling thresholds predicted by the continuum description are in good agreement with the results of stability calculations based on the vertex model. Our results establish a direct connection between discrete and continuum descriptions of cell sheets and can be used to probe a wide range of morphogenetic processes in epithelial tissues.
 
2014
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.
9
Correlated Lateral Diffusion of Lipids - Adrien, Vladimir and Rayan, Gamal and Taulier, Nicolas and Urbach, Wladimir
BIOPHYSICAL JOURNAL 10684A (2014)
DOI
10
Surfactant Bilayers Maintain Transmembrane Protein Activity - Rayan, Gamal and Adrien, Vladimir and Reffay, Myriam and Picard, Martin and Ducruix, Arnaud and Schmutz, Marc and Urbach, Wladimir and Taulier, Nicolas
BIOPHYSICAL JOURNAL 1071129-1135 (2014)

Abstract : In vitro studies of membrane proteins are of interest only if their structure and function are significantly preserved. One approach is to insert them into the lipid bilayers of highly viscous cubic phases rendering the insertion and manipulation of proteins difficult. Less viscous lipid sponge phases are sometimes used, but their relatively narrow domain of existence can be easily disrupted by protein insertion. We present here a sponge phase consisting of nonionic surfactant bilayers. Its extended domain of existence and its low viscosity allow easy insertion and manipulation of membrane proteins. We show for the first time, to our knowledge, that transmennbrane proteins, such as bacteriorhodopsin, sarcoplasmic reticulum Ca(2+)ATPase (SERCA1a), and its associated enzymes, are fully active in a surfactant phase.
 
2013
11
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.
BIOPHYSICAL JOURNAL 104367A-368A (2013)
12
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
BIOPHYSICAL JOURNAL 10444A (2013)
 
2012
13
Lateral Diffusion and Association of Transmembrane Proteins Inside a Biomimetic Bilayer Mesophase - Rayan, Gamal and Reffay, Myriam and Picard, Martin and Taulier, Nicolas and Ducruix, Arnaud and Urbach, Wladimir
BIOPHYSICAL JOURNAL 102625A (2012)
DOI
14
Different Cell Fates from Cell-Cell Interactions: Core Architectures of Two-Cell Bistable Networks - Rouault, Herve and Hakim, Vincent
BIOPHYSICAL JOURNAL 102417-426 (2012)

Abstract : The acquisition of different fates by cells that are initially in the same state is central to development. Here, we investigate the possible structures of bistable genetic networks that can allow two identical cells to acquire different fates through cell-cell interactions. Cell-autonomous bistable networks have been previously sampled using an evolutionary algorithm. We extend this evolutionary procedure to take into account interactions between cells. We obtain a variety of simple bistable networks that we classify into major subtypes. Some have long been proposed in the context of lateral inhibition through the Notch-Delta pathway, some have been more recently considered and others appear to be new and based on mechanisms not previously considered. The results highlight the role of posttranscriptional interactions and particularly of protein complexation and sequestration, which can replace cooperativity in transcriptional interactions. Some bistable networks are entirely based on posttranscriptional interactions and the simplest of these is found to lead, upon a single parameter change, to oscillations in the two cells with opposite phases. We provide qualitative explanations as well as mathematical analyses of the dynamical behaviors of various created networks. The results should help to identify and understand genetic structures implicated in cell-cell interactions and differentiation.
 
2011
15
A versatile Bilayer Phase for the Studies of Transmembrane Proteins' Association - Rayan, Gamal and Reffay, Myriam and Picard, Martin and Taulier, Nicolas and Ducruix, Arnaud and Urbach, Wladimir
BIOPHYSICAL JOURNAL 100359 (2011)
DOI
16
Improving Signal/Noise Resolution in Single-Molecule Experiments Using Molecular Constructs with Short Handles - Forns, N. and de Lorenzo, S. and Manosas, M. and Hayashi, K. and Huguet, J. M. and Ritort, F.
BIOPHYSICAL JOURNAL 1001765-1774 (2011)

Abstract : We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately enhances the signal/noise ratio (SNR) in hopping experiments as compared to conventional long-handled constructs (congruent to 700 bp). The shorter construct results in a signal of higher SNR and slower folding/unfolding kinetics, thereby facilitating the detection of otherwise fast structural transitions. A novel analysis, as far as we are aware, of the elastic properties of the molecular setup, based on high-bandwidth measurements of force fluctuations along the folded branch, reveals that the highest SNR that can be achieved with short handles is potentially limited by the marked reduction of the effective persistence length and stretch modulus of the short linker complex.
 
2010
17
Modulation of the Lateral Mobility of Transmembrane Peptides with Hydrophobic Mismatch - Gambin, Yann and Reffay, Myriam and Sierecki, Emma and Homble, Francois and Genest, Marc and Hodges, Robert S. and Gov, Nir and Taulier, Nicolas and Urbach, Wladimir
BIOPHYSICAL JOURNAL 98224A-225A (2010)
18
Coupling DNA Unwinding Activity With Primer Synthesis in the Bacteriophage T4 Primosome - Croquette, Vincent and Manosas, Maria and Spiering, Michelle M. and Zhuang, Zhihao and Benkovic, Stephen J.
BIOPHYSICAL JOURNAL 9866A-67A (2010)
19
Surfactant Sponge Phase Is a Versatile, Tunable and Biologically Relevant Medium To Study Membrane Protein Interactions - Picard, Martin and Rayan, Gamal and Taulier, Nicolas and Broutin, Isabelle and Ducruix, Arnaud and Urbach, Wladimir
BIOPHYSICAL JOURNAL 9859A (2010)
20
Transmembrane Protein Association in a Biomimetic Medium - Rayan, Gamal and Reffay, Myriam and Picard, Martin and Taulier, Nicolas and Ducruix, Arnaud and Urbach, Wladimir
BIOPHYSICAL JOURNAL 9849A-50A (2010)