Glassy behavior of a homopolymer from molecular dynamics simulations

We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the theta point, and the structure factor, as a function of time. The observation of these quantities show a close resemblance to those measured in structural glasses and suggest that the polymer chain in its low temperature phase is in a glassy phase, with its dynamics dominated by traps. In equilibrium, at low temperature, we observe the trapping of the monomers and a slowing down of the overall motion of the polymer as well as non-exponential relaxation of the structure factor. In out-of-equilibrium, at low temperatures, we compute the two-time quantities and observe breaking of ergodicity in a range of waiting times, with the onset of aging.Comment: 11 pages, 4 figure

Investigation of qq-dependent dynamical heterogeneity in a colloidal gel by x-ray photon correlation spectroscopy

We use time-resolved X-Photon Correlation Spectroscopy to investigate the slow dynamics of colloidal gels made of moderately attractive carbon black particles. We show that the slow dynamics is temporally heterogeneous and quantify its fluctuations by measuring the variance $\chi$ of the instantaneous intensity correlation function. The amplitude of dynamical fluctuations has a non-monotonic dependence on scattering vector $q$, in stark contrast with recent experiments on strongly attractive colloidal gels [Duri and Cipelletti, \textit{Europhys. Lett.} \textbf{76}, 972 (2006)]. We propose a simple scaling argument for the $q$-dependence of fluctuations in glassy systems that rationalizes these findings.Comment: Final version published in PR

Collapse Dynamics of a Homopolymer: Theory and Simulation

We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each containing g ~ t monomers. These segments are statistical quantities representing cylinders of length R ~ t^{1/2} and diameter d ~ t^{1/4}, but structured out of stretched arrays of spherical globules. This prescription incorporates the capillary instability. We compare the time-dependent structure factor derived for our theory with that obtained from ultra-large-scale molecular dynamics simulation with explicit solvent. This is the first time such a detailed comparison of theoretical and simulation predictions of collapsing chain structure has been attempted. The favorable agreement between the theoretical and computed structure factors supports the picture of the coarse-graining process during polymer collapse.Comment: 4 pages, 3 figure

Dynamic first-order phase transition in kinetically constrained models of glasses

We show that the dynamics of kinetically constrained models of glass formers takes place at a first-order coexistence line between active and inactive dynamical phases. We prove this by computing the large-deviation functions of suitable space-time observables, such as the number of configuration changes in a trajectory. We present analytic results for dynamic facilitated models in a mean-field approximation, and numerical results for the Fredrickson-Andersen model, the East model, and constrained lattice gases, in various dimensions. This dynamical first-order transition is generic in kinetically constrained models, and we expect it to be present in systems with fully jammed states.Comment: 4.1 pages, 3 figure

ASS1 Overexpression: A Hallmark of Sonic Hedgehog Hepatocellular Adenomas; Recommendations for Clinical Practice.

Until recently, 10% of hepatocellular adenomas (HCAs) remained unclassified (UHCA). Among the UHCAs, the sonic hedgehog HCA (shHCA) was defined by focal deletions that fuse the promoter of Inhibin beta E chain with GLI1. Prostaglandin D2 synthase was proposed as immunomarker. In parallel, our previous work using proteomic analysis showed that most UHCAs constitute a homogeneous subtype associated with overexpression of argininosuccinate synthase (ASS1). To clarify the use of ASS1 in the HCA classification and avoid misinterpretations of the immunohistochemical staining, the aims of this work were to study (1) the link between shHCA and ASS1 overexpression and (2) the clinical relevance of ASS1 overexpression for diagnosis. Molecular, proteomic, and immunohistochemical analyses were performed in UHCA cases of the Bordeaux series. The clinico-pathological features, including ASS1 immunohistochemical labeling, were analyzed on a large international series of 67 cases. ASS1 overexpression and the shHCA subgroup were superimposed in 15 cases studied by molecular analysis, establishing ASS1 overexpression as a hallmark of shHCA. Moreover, the ASS1 immunomarker was better than prostaglandin D2 synthase and only found positive in 7 of 22 shHCAs. Of the 67 UHCA cases, 58 (85.3%) overexpressed ASS1, four cases were ASS1 negative, and in five cases ASS1 was noncontributory. Proteomic analysis performed in the case of doubtful interpretation of ASS1 overexpression, especially on biopsies, can be a support to interpret such cases. ASS1 overexpression is a specific hallmark of shHCA known to be at high risk of bleeding. Therefore, ASS1 is an additional tool for HCA classification and clinical diagnosis

First-order dynamical phase transition in models of glasses: an approach based on ensembles of histories

We investigate the dynamics of kinetically constrained models of glass formers by analysing the statistics of trajectories of the dynamics, or histories, using large deviation function methods. We show that, in general, these models exhibit a first-order dynamical transition between active and inactive dynamical phases. We argue that the dynamical heterogeneities displayed by these systems are a manifestation of dynamical first-order phase coexistence. In particular, we calculate dynamical large deviation functions, both analytically and numerically, for the Fredrickson-Andersen model, the East model, and constrained lattice gas models. We also show how large deviation functions can be obtained from a Landau-like theory for dynamical fluctuations. We discuss possibilities for similar dynamical phase-coexistence behaviour in other systems with heterogeneous dynamics.Comment: 29 pages, 7 figs, final versio

Dynamics of Collapse of flexible Polyelectrolytes and Polyampholytes

We provide a theory for the dynamics of collapse of strongly charged polyelectrolytes (PEs) and flexible polyampholytes (PAs) using Langevin equation. After the initial stage, in which counterions condense onto PE, the mechanism of approach to the globular state is similar for PE and PA. In both instances, metastable pearl-necklace structures form in characteristic time scale that is proportional to N^{4/5} where N is the number of monomers. The late stage of collapse occurs by merger of clusters with the largest one growing at the expense of smaller ones (Lifshitz- Slyozov mechanism). The time scale for this process T_{COLL} N. Simulations are used to support the proposed collapse mechanism for PA and PE.Comment: 14 pages, 2 figure

Capillary condensation in disordered porous materials: hysteresis versus equilibrium behavior

We study the interplay between hysteresis and equilibrium behavior in capillary condensation of fluids in mesoporous disordered materials via a mean-field density functional theory of a disordered lattice-gas model. The approach reproduces all major features observed experimentally. We show that the simple van der Waals picture of metastability fails due to the appearance of a complex free-energy landscape with a large number of metastable states. In particular, hysteresis can occur both with and without an underlying equilibrium transition, thermodynamic consistency is not satisfied along the hysteresis loop, and out-of-equilibrium phase transitions are possible.Comment: 4 pages, 4 figure

Structure factor of polymers interacting via a short range repulsive potential: application to hairy wormlike micelles

We use the Random Phase Approximation (RPA) to compute the structure factor, S(q), of a solution of chains interacting through a soft and short range repulsive potential V. Above a threshold polymer concentration, whose magnitude is essentially controlled by the range of the potential, S(q) exhibits a peak whose position depends on the concentration. We take advantage of the close analogy between polymers and wormlike micelles and apply our model, using a Gaussian function for V, to quantitatively analyze experimental small angle neutron scattering profiles of semi-dilute solutions of hairy wormlike micelles. These samples, which consist in surfactant self-assembled flexible cylinders decorated by amphiphilic copolymer, provide indeed an appropriate experimental model system to study the structure of sterically interacting polymer solutions