3,514 research outputs found
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 and density of
obstacles as control parameters. A two-step decay is observed for large
values of and , 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
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