Dynamics of a rod in a homogeneous/inhomogeneous frozen disordered medium: Correlation functions and non-Gaussian effects

We present molecular dynamics simulations of the motion of a single rigid rod in a disordered static 2d-array of disk-like obstacles. Two different configurations have been used for the latter: A completely random one, and which thus has an inhomogeneous structure, and an homogeneous ``glassy'' one, obtained from freezing a liquid of soft disks in equilibrium. Small differences are observed between both structures for the translational dynamics of the rod center-of-mass. In contrast to this, the rotational dynamics in the glassy host medium is strongly slowed down in comparison with the random one. We calculate angular correlation functions for a wide range of rod length $L$ and density of obstacles $\rho$ as control parameters. A two-step decay is observed for large values of $L$ and $\rho$, in analogy with supercooled liquids at temperature close to the glass transition. In agreement with the prediction of the Mode Coupling Theory, a time-length and time-density scaling is obtained. In order to get insight on the relation between the heterogeneity of the dynamics and the structure of the host medium, we determine the deviations from Gaussianity at different length scales. Strong deviations are obtained even at spatial scales much larger than the rod length. The magnitude of these deviations is independent of the nature of the host medium. This result suggests that the large scale translational dynamics of the rod is affected only weakly by the presence of inhomogeneities in the host medium.Comment: Published in AIP Conference Proceedings 708 (2004) 576-58

A population-based microbial oscillator

Genetic oscillators are a major theme of interest in the emerging field of synthetic biology. Until recently, most work has been carried out using intra-cellular oscillators, but this approach restricts the broader applicability of such systems. Motivated by a desire to develop large-scale, spatially-distributed cell-based computational systems, we present an initial design for a population-level oscillator which uses three different bacterial strains. Our system is based on the client-server model familiar to computer science, and uses quorum sensing for communication between nodes. We present the results of extensive in silico simulation tests, which confirm that our design is both feasible and robust.Comment: Submitte

Logarithmic Relaxation in a Kinetically Constrained Model

We present Monte Carlo simulations in a modification of the north-or-east-or-front model recently investigated by Berthier and Garrahan [J. Phys. Chem. B 109, 3578 (2005)]. In this coarse-grained model for relaxation in supercooled liquids, the liquid structure is substituted by a three-dimensional array of cells. A spin variable is assigned to each cell, with values 0 or 1 denoting respectively unexcited and excited local states in a mobility field. Change in local mobility (spin flip) for a given cell is permitted according to kinetic constraints determined by the mobilities of neighboring cells. In this work we keep the same kinetic constraints of the original model, but we introduce two types of cells (denoted as "fast'' and "slow'') with very different rates for spin flip. As a consequence, fast and slow cells exhibit very different relaxation times for spin correlators. While slow cells exhibit standard relaxation, fast cells display anomalous relaxation, characterized by a concave-to-convex crossover in spin correlators by changing temperature or composition. At intermediate state points logarithmic relaxation is observed over three time decades. These results display striking analogies with dynamic correlators reported in recent simulations on a bead-spring model for polymer blends.Comment: Major changes. To be published in Journal of Chemical Physic

Diffusion and Relaxation Dynamics in Cluster Crystals

For a large class of fluids exhibiting ultrasoft bounded pair potentials, particles form crystals consisting of clusters located in the lattice sites, with a density-independent lattice constant. Here we present an investigation on the dynamic features of a representative example of this class. It is found that particles can diffuse between lattice sites, maintaining the lattice structure, through an activated hopping mechanism. This feature yields finite values for the diffusivity and full relaxation of density correlation functions. Simulations suggest the existence of a localization transition which is avoided by hopping, and a dynamic decoupling between self- and collective correlations.Comment: 4 pages, 7 figure

Static and dynamic contributions to anomalous chain dynamics in polymer blends

By means of computer simulations, we investigate the relaxation of the Rouse modes in a simple bead-spring model for non-entangled polymer blends. Two different models are used for the fast component, namely fully-flexible and semiflexible chains. The latter are semiflexible in the meaning that static intrachain correlations are strongly non-gaussian at all length scales. The dynamic asymmetry in the blend is strongly enhanced by decreasing temperature, inducing confinement effects on the fast component. The dynamics of the Rouse modes show very different trends for the two models of the fast component. For the fully-flexible case, the relaxation times exhibit a progressive deviation from Rouse scaling on increasing the dynamic asymmetry. This anomalous effect has a dynamic origin. It is not related to particular static features of the Rouse modes, which indeed are identical to those of the fully-flexible homopolymer, and are not modified by the dynamic asymmetry in the blend. On the contrary, in the semiflexible case the relaxation times exhibit approximately the same scaling behaviour as the amplitudes of the modes. This suggests that the origin of the anomalous dynamic scaling for semiflexible chains confined in the blend is esentially of static nature. We discuss implications of these observations for the applicability of theoretical approaches to chain dynamics in polymer blends.Comment: 15 pages (single-column), 6 figure