laboratoire de physique statistique
 
 
laboratoire de physique statistique

Publications

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JOURNAL OF PHYSICAL CHEMISTRY B 


8
P U B L I C A T I O N S



 
2016
Modeling the Kinetics of Open Self-Assembly - Verdier, Timothee and Foret, Lionel and Castelnovo, Martin
JOURNAL OF PHYSICAL CHEMISTRY B 1206411-6420 (2016)

Abstract : In this work, we explore theoretically the kinetics of molecular self-assembly in the presence of constant monomer flux as an input, and a maximal size. The proposed model is supposed to reproduce the dynamics of viral self-assembly for enveloped virus. It turns out that the kinetics of open self-assembly is rather quantitatively different from the kinetics of similar closed assembly. In particular, our results show that the convergence toward the stationary state is reached through assembly waves. Interestingly, we show that the production of complete clusters is much more efficient in the presence of a constant input flux, rather than providing all monomers at the beginning of the self-assembly.
 
2013
Effect of Phenotypic Selection on Stochastic Gene Expression - Mora, Thierry and Walczak, Aleksandra M.
JOURNAL OF PHYSICAL CHEMISTRY B 11713194-13205 (2013)

Abstract : Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a description based on discrete phenotypic states. Here, we consider the effects of selection acting on a single trait, which we explicitly link to the variable number of proteins expressed by a gene. Considering different regulatory models for the gene under selection, we calculate the steady-state distribution of expression levels and show how the population adapts its expression to enhance its fitness. We quantitatively relate the overall fitness of the population to the heritability of expression levels and their diversity within the population. We show how selection can increase or decrease the variability in the population, alter the stability of bimodal states, and impact the switching rates between metastable attractors.
Exact Theory of Dense Amorphous Hard Spheres in High Dimension. II. The High Density Regime and the Gardner Transition - Kurchan, Jorge and Parisi, Giorgio and Urbani, Pierfrancesco and Zamponi, Francesco
JOURNAL OF PHYSICAL CHEMISTRY B 11712979-12994 (2013)

Abstract : We consider the theory of the glass phase and jamming of hard spheres in the large space dimension limit. Building upon the exact expression for the free-energy functional obtained previously, we find that the random first order transition (RFOT) scenario is realized here with two thermodynamic transitions: the usual Kauzmann point associated with entropy crisis and a further transition at higher pressures in which a glassy structure of microstates is developed within each amorphous state. This kind of glass-glass transition into a phase dominating the higher densities was described years ago by Elisabeth Gardner, and may well be a generic feature of RFOT. Microstates that are small excitations of an amorphous matrix-separated by low entropic or energetic barriers-thus emerge naturally, and modify the high pressure (or low temperature) limit of the thermodynamic functions.
 
2012
Laser-Heating-Induced Displacement of Surfactants on the Water Surface - Backus, Ellen H. G. and Bonn, Daniel and Cantin, Sophie and Roke, Sylvie and Bonn, Mischa
JOURNAL OF PHYSICAL CHEMISTRY B 1162703-2712 (2012)

Abstract : We report a combined vibrational sum-frequency generation (SFG) spectroscopy, Brewster angle microscopy (BAM), and ellipsometry study of different surfactants on water as a function of surfactant density. Vibrational SFG spectra of surfactants on the water surface in a Langmuir trough have been measured in both the surfactant CH and the water OH stretch regions. At low densities, the SFG signal generated at the surface in the presence of the surfactant is indistinguishable from the SFG signal generated at the clean water air interface. When the surfactant density increases, i.e., upon compressing the monolayer, a very sudden increase in the SFG signal in both the CH and OH spectral regions is observed. For higher laser fluences, this stepwise increase occurs at increasingly higher surfactant densities. Since BAM shows that surfactant molecules are clearly present at these low densities, we conclude that at low surfactant density the laser beam displaces relatively high-density domains with surfactants in the liquid expanded phase out of the region of the laser focus. This is a consequence of the thermal gradient induced by local heating of the water phase with the monolayer on top due to repetitive laser excitation at 1 kHz. It can be circumvented by using a rotating trough. In this manner, the sampled surface area can be refreshed, allowing artifact-free vibrational SFG spectra to be measured down to the very lowest surfactant densities. In ellipsometry experiments, a similar step can be noticed, which, however, is of a different nature; i.e., it is not related to heating (the laser fluence is very low and the light nonresonant) but to a molecular transition. The occurrence of the step in ellipsometry as a function of area per molecule depends critically on the preparation of the monolayer. By giving the molecules time and space to relax during the preparation of the monolayer, this step could also be eliminated.
 
2011
Cavitation in Heavy Water and Other Liquids - Arvengas, Arnaud and Herbert, Eric and Cersoy, Sophie and Davitt, Kristina and Caupin, Frederic
JOURNAL OF PHYSICAL CHEMISTRY B 11514240-14245 (2011)

Abstract : We report on measurements of the cavitation pressure in several liquids subjected to tension in an acoustic wave and compare the results to classical nucleation theory (CNT). This study is motivated by the sizable discrepancy between the acoustic cavitation threshold measured in water and the value predicted by CNT. We find that the same discrepancy is present for heavy g water, whereas the agreement is better for ethanol and heptane and intermediate in the case of dimethyl sulfoxide. It is well-known that water is an anomalous liquid, a consequence of its hydrogen-bonded network. The other liquids studied represent very different molecular interactions. Our results indicate that the cavitation threshold approaches the prediction of CNT as the surface Conversely, this raises the question of the validity of a simple theory such as CNT to account for high surface tension liquids and suggests that an appropriate microscopic model of such liquids may be necessary to correctly predict the cavitation threshold.
 
2010
Variation of the Lateral Mobility of Transmembrane Peptides with Hydrophobic Mismatch - Gambin, Yann and Reffay, Myriam and Sierecki, Emma and Homble, Fabrice and Hodges, Robert S. and Gov, Nir S. and Taulier, Nicolas and Urbach, Wladimir
JOURNAL OF PHYSICAL CHEMISTRY B 1143559-3566 (2010)

Abstract : A hydrophobic mismatch between protein length and membrane thickness call lead to a modification of protein conformation, function, and oligomerization. To study the role of hydrophobic mismatch, we have measured the change in mobility of transmembrane peptides possessing a hydrophobic helix of various length d(pi), ill lipid membranes of giant vesicles. We also used a model system where the hydrophobic thickness of the bilayers, h, call be tuned at Will. We precisely Measured the diffusion coefficient of the embedded peptides and gained access to the apparent size of diffusing, objects. For bilayers thinner than d(pi) diffusion coefficient decreases, and the derived characteristic sizes are larger than the peptide radii. Previous studies Suggest that peptides accommodate by tilting. This scenario was confirmed by ATR-FTIR spectroscopy. As the membrane thickness increases, the value of the diffusion coefficient increases to reach a maximum at h approximate to d(pi). We show that this variation ill diffusion Coefficient is consistent with a decrease in peptide tilt. To do so, we have derived a relation between the diffusion coefficient and the tilt angle, and We used this relation to derive the peptide tilt from our diffusion measurements. As the membrane thickness increases, the peptides raise (i.e., their tilt is reduced) and reach all upright position and a maximal mobility for h approximate to d(pi). Using accessibility measurements, we show that when the membrane becomes too thick, the peptide polar heads sink into the interfacial region. Surprisingly, this ``pinching'' behavior does not hinder the lateral diffusion of the transmembrane peptides. Ultimately, a break in the peptide transmembrane anchorage is observed and is revealed by a ``jump'' in the D values.
 
2009
Helix-Coil Transition of DNA Monitored by Pressure Perturbation Calorimetry - Rayan, Gamal and Tsamaloukas, Alekos D. and Macgregor, Jr., Robert B. and Heerklotz, Heiko
JOURNAL OF PHYSICAL CHEMISTRY B 1131738-1742 (2009)

Abstract : We report the first use of pressure perturbation calorimetry (PPC) to characterize the heat-induced helix-coil transition of DNA polymers. The alternating copolymer poly[d(A-T)] was studied in aqueous solutions containing 5.2 and 18.2 mM Na(+); it exhibited helix-coil transition temperatures of 33.6 and 44.7 degrees C, respectively. The transition is accompanied by a negative molar volume change, Delta V = -2.6 and -2.1 mL/mol (base pair), respectively, and an increase in the coefficient of thermal expansion, Delta alpha = +5 x 10(-4) K(-1) (at both ionic strengths). These values are consistent with a greater hydration of the coil form. The larger water-accessible surface area of the coil causes more water molecules to assume a bound, more densely packed structure that then gradually decreases with increasing temperature, leading to a larger value of alpha. The magnitude of the volume changes detected by PPC were larger than those deduced from high-pressure UV spectroscopy, shedding light on the effect of pressure on Delta V. The shape of the PPC peak was nearly identical to the shape of the DSC peak, providing direct evidence for the correlation between the molar volume change and enthalpy change for the helix to coil transition of DNA.
Thin Nematic Films on Liquid Substrates - Deabre, U. and Richard, C. and Cazabat, A. M.
JOURNAL OF PHYSICAL CHEMISTRY B 1133647-3652 (2009)

Abstract : Thin films of cyanobiphenyl liquid crystals (nCB) deposited on water or glycerol have been studied in the nematic temperature range. A common property of the systems is the hybrid anchoring conditions at the film interfaces. The preferred orientation of the nematic director is planar at the liquid interface, and it is homeotropic and somewhat weaker at the air interface. The resulting structure of the film depends on its thickness. Films thicker than 0.5 mu m show the usual defects of nematics. Between 0.5 mu m and 20-30 nm, complex instability patterns such as stripes, ``chevrons'', or squares are observed in extended films. Then there is a forbidden range of thickness below in which much thinner structures (usually monolayers and trilayers) are present. The present paper investigates this common behavior in various systems and gives arguments for its analysis.