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 $\tau$ diverges as the packing fraction $\phi$ approaches a threshold related to percolation, while for short-lived bonds, the $\phi$-dependence of $\tau$ is more typical of a glassy system. At intermediate bond lifetimes, the $\phi$-dependence of $\tau$ is driven by percolation at low $\phi$, but then crosses over to glassy behavior at higher $\phi$. 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