226 research outputs found
Distributions of inherent structure energies during aging
We perform extensive simulations of a binary mixture Lennard-Jones system
subjected to a temperature jump in order to study the time evolution of
fluctuations during aging. Analyzing data from 1500 different aging
realizations, we calculate distributions of inherent structure energies for
different aging times and contrast them with equilibrium. We find that the
distributions initially become narrower and then widen as the system
equilibrates. For deep quenches, fluctuations in the glassy system differ
significantly from those observed in equilibrium. Simulation results are
partially captured by theoretical predictions only when the final temperature
is higher than the mode coupling temperature.Comment: 5 pages, 4 figure
Effect of bond lifetime on the dynamics of a short-range attractive colloidal system
We perform molecular dynamics simulations of short-range attractive colloid
particles modeled by a narrow (3% of the hard sphere diameter) square well
potential of unit depth. We compare the dynamics of systems with the same
thermodynamics but different bond lifetimes, by adding to the square well
potential a thin barrier at the edge of the attractive well. For permanent
bonds, the relaxation time diverges as the packing fraction
approaches a threshold related to percolation, while for short-lived bonds, the
-dependence of is more typical of a glassy system. At intermediate
bond lifetimes, the -dependence of is driven by percolation at low
, but then crosses over to glassy behavior at higher . We also
study the wavevector dependence of the percolation dynamics.Comment: Revised; 9 pages, 9 figure
Molecular structural order and anomalies in liquid silica
The present investigation examines the relationship between structural order,
diffusivity anomalies, and density anomalies in liquid silica by means of
molecular dynamics simulations. We use previously defined orientational and
translational order parameters to quantify local structural order in atomic
configurations. Extensive simulations are performed at different state points
to measure structural order, diffusivity, and thermodynamic properties. It is
found that silica shares many trends recently reported for water [J. R.
Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate
densities, the distribution of local orientational order is bimodal. At fixed
temperature, order parameter extrema occur upon compression: a maximum in
orientational order followed by a minimum in translational order. Unlike water,
however, silica's translational order parameter minimum is broad, and there is
no range of thermodynamic conditions where both parameters are strictly
coupled. Furthermore, the temperature-density regime where both structural
order parameters decrease upon isothermal compression (the structurally
anomalous regime) does not encompass the region of diffusivity anomalies, as
was the case for water.Comment: 30 pages, 8 figure
Simulation of a two-dimensional model for colloids in a uniaxial electric field
We perform Monte Carlo simulations of a simplified two-dimensional model for
colloidal hard spheres in an external uniaxial AC electric field.
Experimentally, the external field induces dipole moments in the colloidal
particles, which in turn form chains. We therefore approximate the system as
composed of well formed chains of dipolar hard spheres of a uniform length. The
dipolar interaction between colloidal spheres gives rise to an effective
interaction between the chains, which we treat as disks in a plane, that
includes a short range attraction and long range repulsion. Hence, the system
favors finite clustering over bulk phase separation and indeed we observe at
low temperature and density that the system does form a cluster phase. As
density increases, percolation is accompanied by a pressure anomaly. The
percolated phase, despite being composed of connected, locally crystalline
domains, does not bear the typical signatures of a hexatic phase. At very low
densities, we find no indication of a "void phase" with a cellular structure
seen recently in experiments.Comment: 10 pages, 14 figure
Potential Energy Landscape Equation of State
Depth, number, and shape of the basins of the potential energy landscape are
the key ingredients of the inherent structure thermodynamic formalism
introduced by Stillinger and Weber [F. H. Stillinger and T. A. Weber, Phys.
Rev. A 25, 978 (1982)]. Within this formalism, an equation of state based only
on the volume dependence of these landscape properties is derived. Vibrational
and configurational contributions to pressure are sorted out in a transparent
way. Predictions are successfully compared with data from extensive molecular
dynamics simulations of a simple model for the fragile liquid orthoterphenyl.Comment: RevTeX4, 4 pages, 5 figure
The network topology of a potential energy landscape: A static scale-free network
Here we analyze the topology of the network formed by the minima and
transition states on the potential energy landscape of small clusters. We find
that this network has both a small-world and scale-free character. In contrast
to other scale-free networks, where the topology results from the dynamics of
the network growth, the potential energy landscape is a static entity.
Therefore, a fundamentally different organizing principle underlies this
behaviour: The potential energy landscape is highly heterogeneous with the
low-energy minima having large basins of attraction and acting as the
highly-connected hubs in the network.Comment: 4 pages, 4 figures, revtex
Optical Activity of a Neutrino Gas
For photons that propagate through a gas of neutrinos with a non-zero
chemical potential, the left-handed and right-handed polarization modes acquire
different dispersion relations. This is due to the CP and CPT-odd terms induced
by such a background on the photon self-energy. We present a detailed
calculation of this effect, which does not depend on any physical assumptions
beyond those of the standard electroweak model. Some possible cosmological and
astrophysical implications of our results are considered in several contexts,
including the recent discussions regarding the rotation of the plane of
polarization of electromagnetic waves over cosmological distances.Comment: latex, axodra
Modification of Collagen by 3-Deoxyglucosone Alters Wound Healing through Differential Regulation of p38 MAP Kinase
Background: Wound healing is a highly dynamic process that requires signaling from the extracellular matrix to the fibroblasts for migration and proliferation, and closure of the wound. This rate of wound closure is impaired in diabetes, which may be due to the increased levels of the precursor for advanced glycation end products, 3-deoxyglucosone (3DG). Previous studies suggest a differential role for p38 mitogen-activated kinase (MAPK) during wound healing; whereby, p38 MAPK acts as a growth kinase during normal wound healing, but acts as a stress kinase during diabetic wound repair. Therefore, we investigated the signaling cross-talk by which p38 MAPK mediates wound healing in fibroblasts cultured on native collagen and 3DG-collagen. Methodology/Principal Findings: Using human dermal fibroblasts cultured on 3DG-collagen as a model of diabetic wounds, we demonstrated that p38 MAPK can promote either cell growth or cell death, and this was dependent on the activation of AKT and ERK1/2. Wound closure on native collagen was dependent on p38 MAPK phosphorylation of AKT and ERK1/2. Furthermore, proliferation and collagen production in fibroblasts cultured on native collagen was dependent on p38 MAPK regulation of AKT and ERK1/2. In contrast, 3DG-collagen decreased fibroblast migration, proliferation, and collagen expression through ERK1/2 and AKT downregulation via p38 MAPK. Conclusions/Significance: Taken together, the present study shows that p38 MAPK is a key signaling molecule that plays
Glass Transition Behavior of Polymer Films of Nanoscopic Dimensions
Glass transition behavior of nanoscopically thin polymer films is
investigated by means of molecular dynamics simulations. A thin polymer film
that is composed of bead-spring model chains and supported on an idealized, fcc
lattice substrate surface is studied in this work.Comment: in review, macromolecule
Lumican Expression in Diaphragm Induced by Mechanical Ventilation
Diaphragmatic dysfunction found in the patients with acute lung injury required prolonged mechanical ventilation. Mechanical ventilation can induce production of inflammatory cytokines and excess deposition of extracellular matrix proteins via up-regulation of transforming growth factor (TGF)-β1. Lumican is known to participate in TGF-β1 signaling during wound healing. The mechanisms regulating interactions between mechanical ventilation and diaphragmatic injury are unclear. We hypothesized that diaphragmatic damage by short duration of mechanical stretch caused up-regulation of lumican that modulated TGF-β1 signaling.Male C57BL/6 mice, either wild-type or lumican-null, aged 3 months, weighing between 25 and 30 g, were exposed to normal tidal volume (10 ml/kg) or high tidal volume (30 ml/kg) mechanical ventilation with room air for 2 to 8 hours. Nonventilated mice served as control groups.High tidal volume mechanical ventilation induced interfibrillar disassembly of diaphragmatic collagen fiber, lumican activation, type I and III procollagen, fibronectin, and α-smooth muscle actin (α-SMA) mRNA, production of free radical and TGF-β1 protein, and positive staining of lumican in diaphragmatic fiber. Mechanical ventilation of lumican deficient mice attenuated diaphragmatic injury, type I and III procollagen, fibronectin, and α-SMA mRNA, and production of free radical and TGF-β1 protein. No significant diaphragmatic injury was found in mice subjected to normal tidal volume mechanical ventilation.Our data showed that high tidal volume mechanical ventilation induced TGF-β1 production, TGF-β1-inducible genes, e.g., collagen, and diaphragmatic dysfunction through activation of the lumican
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