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

Correlated percolation models of structured habitat in ecology

Percolation offers acknowledged models of random media when the relevant medium characteristics can be described as a binary feature. However, when considering habitat modeling in ecology, a natural constraint comes from nearest-neighbor correlations between the suitable/unsuitable states of the spatial units forming the habitat. Such constraints are also relevant in the physics of aggregation where underlying processes may lead to a form of correlated percolation. However, in ecology, the processes leading to habitat correlations are in general not known or very complex. As proposed by Hiebeler [Ecology {\bf 81}, 1629 (2000)], these correlations can be captured in a lattice model by an observable aggregation parameter $q$, supplementing the density $p$ of suitable sites. We investigate this model as an instance of correlated percolation. We analyze the phase diagram of the percolation transition and compute the cluster size distribution, the pair-connectedness function $C(r)$ and the correlation function $g(r)$. We find that while $g(r)$ displays a power-law decrease associated with long-range correlations in a wide domain of parameter values, critical properties are compatible with the universality class of uncorrelated percolation. We contrast the correlation structures obtained respectively for the correlated percolation model and for the Ising model, and show that the diversity of habitat configurations generated by the Hiebeler model is richer than the archetypal Ising model. We also find that emergent structural properties are peculiar to the implemented algorithm, leading to questioning the notion of a well-defined model of aggregated habitat. We conclude that the choice of model and algorithm have strong consequences on what insights ecological studies can get using such models of species habitat

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

Ethane-beta-Sultam Modifies the Activation of the Innate Immune System Induced by Intermittent Ethanol Administration in Female Adolescent Rats

Intermittent ethanol abuse or ‘binge drinking’ during adolescence induces neuronal damage, which may be associated with cognitive dysfunction. To investigate the neurochemical processes involved, rats were administered either 1 g/kg or 2 g/kg ethanol in a ‘binge drinking’ regime. After only 3 weeks, significant activation of phagocytic cells in the peripheral (alveolar macrophages) and the hippocampal brain region (microglia cells) was present,as exemplified by increases in the release of pro-inflammatory cytokines in the macrophages and of iNOS in the microglia. This was associated with neuronal loss in the hippocampus CA1 region. Daily supplementation with a taurine prodrug, ethane-β-sultam, 0.028 g/kg, during the intermittent ethanol loading regime, supressed the release of the pro-inflammatory cytokines and of reactive nitrogen species, as well as neuronal loss, particularly in the rats administered the lower dose of ethanol, 1 g/kg. Plasma, macrophage and hippocampal taurine levels increased marginally after ethane-β-sultam supplementation. The ‘binge drinking’ ethanol rats administered 1 g/kg ethanol showed increased latencies to those of the control rats in their acquisition of spacial navigation in the Morris Water Maze, which was normalised to that of the controls values after ethane-β-sultam administration. Such results confirm that the administration of ethane-β-sultam to binge drinking rats reduces neuroinflammation in both the periphery and the brain, suppresses neuronal loss, and improved working memory of rats in a water maze study

The encapsulation of DNA molecules within biomimetic lipid nanocapsules

Most of DNA synthetic complexes result from the self-assembly of DNA molecules with cationic lipids or polymers in an aqueous controlled medium. However, injection of such self-assembled complexes in medium like blood that differ from that of their formulation leads to strong instability. Therefore, DNA vectors that have physico-chemical properties and structural organisation that will not be sensitive to a completely different medium in terms of ionic and protein composition are actively sought. To this end, the goal here was to discover and optimize a nanostructured system where DNA molecules would be encapsulated in nanocapsules consisting in an oily core and a shell covered by PEG stretches obtained through a nanoemulsion process in the absence of organic solvent. This encapsulation form of DNA molecules would prevent interactions with external hostile biological fluid. The results show the entrapment of lipoplexes into lipid nanocapsules, leading to the formation of neutral 110 nm-DNA nanocapsules. They were weakly removed by the immune system, displaying an increased blood half-life, and improved carcinoma cell transfection, in comparison to the parent lipoplexes. Our results demonstrate that the fabrication of nanocapsules encapsulating hydrophilic DNA in an oily core that meet criteria for blood injection is possible

Folding and unfolding kinetics of a single semiflexible polymer

We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the main contribution to dissipation is from the motion of the domain. In the unfolding transition, dynamic scaling exponents, 1/8 and 1/4, were determined for disentanglement and relaxation steps, respectively. We performed Langevin dynamics simulations to test our theory. It is found that our theory is in good agreement with simulations. We also propose the kinetics of the transitions in the presence of the hydrodynamic interaction.Comment: 12 pages, 10 figure

Injected Power Fluctuations in 1D Dissipative Systems

Using fermionic techniques, we compute exactly the large deviation function (ldf) of the time-integrated injected power in several one-dimensional dissipative systems of classical spins. The dynamics are T=0 Glauber dynamics supplemented by an injection mechanism, which is taken as a Poissonian flipping of one particular spin. We discuss the physical content of the results, specifically the influence of the rate of the Poisson process on the properties of the ldf.Comment: 18 pages, 8 figure