569 research outputs found
Computing the local pressure in molecular dynamics simulations
Computer simulations of inhomogeneous soft matter systems often require
accurate methods for computing the local pressure. We present a simple
derivation, based on the virial relation, of two equivalent expressions for the
local (atomistic) pressure in a molecular dynamics simulation. One of these
expressions, previously derived by other authors via a different route,
involves summation over interactions between particles within the region of
interest; the other involves summation over interactions across the boundary of
the region of interest. We illustrate our derivation using simulations of a
simple osmotic system; both expressions produce accurate results even when the
region of interest over which the pressure is measured is very small.Comment: 11 pages, 4 figure
Short-wavelength collective modes in a binary hard-sphere mixture
We use hard-sphere generalized hydrodynamic equations to discuss the extended
hydrodynamic modes of a binary mixture. The theory presented here is analytic
and it provides us with a simple description of the collective excitations of a
dense binary mixture at molecular length scales. The behavior we predict is in
qualitative agreement with molecular-dynamics results for soft-sphere mixtures.
This study provides some insight into the role of compositional disorder in
forming glassy configurations.Comment: Published; withdrawn since already published. Ordering in the archive
gives misleading impression of new publicatio
Discontinuous Molecular Dynamics for Semi-Flexible and Rigid Bodies
A general framework for performing event-driven simulations of systems with
semi-flexible or rigid bodies interacting under impulsive torques and forces is
outlined. Two different approaches are presented. In the first, the dynamics
and interaction rules are derived from Lagrangian mechanics in the presence of
constraints. This approach is most suitable when the body is composed of
relatively few point masses or is semi-flexible. In the second method, the
equations of rigid bodies are used to derive explicit analytical expressions
for the free evolution of arbitrary rigid molecules and to construct a simple
scheme for computing interaction rules. Efficient algorithms for the search for
the times of interaction events are designed in this context, and the handling
of missed interaction events is discussed.Comment: 16 pages, double column revte
Hydrodynamic Detonation Instability in Electroweak and QCD Phase Transitions
The hydrodynamic stability of deflagration and detonation bubbles for a first
order electroweak and QCD phase transition has been discussed recently with the
suggestion that detonations are stable. We examine here the case of a
detonation more carefully. We find that in front of the bubble wall
perturbations do not grow with time, but behind the wall modes exist which grow
exponentially. We briefly discuss the possible meaning of this instability.Comment: 12 pages, 3 figures available on request, Latex,
FERMILAB--PUB--93/098--
Transport Far From Equilibrium --- Uniform Shear Flow
The BGK model kinetic equation is applied to spatially inhomogeneous states
near steady uniform shear flow. The shear rate of the reference steady state
can be large so the states considered include those very far from equilibrium.
The single particle distribution function is calculated exactly to first order
in the deviations of the hydrodynamic field gradients from their values in the
reference state. The corresponding non-linear hydrodynamic equaitons are
obtained and the set of transport coefficients are identified as explicit
functions of the shear rate. The spectrum of the linear hydrodynamic equation
is studied in detail and qualitative differences from the spectrum for
equilibrium fluctuations are discussed. Conditions for instabilities at long
wavelengths are identified and disccused.Comment: 32 pages, 1 figure, RevTeX, submitted to Phys. Rev.
Long Wavelength Instability for Uniform Shear Flow
Uniform Shear Flow is a prototype nonequilibrium state admitting detailed
study at both the macroscopic and microscopic levels via theory and computer
simulation. It is shown that the hydrodynamic equations for this state have a
long wavelength instability. This result is obtained first from the
Navier-Stokes equations and shown to apply at both low and high densities.
Next, higher order rheological effects are included using a model kinetic
theory. The results are compared favorably to those from Monte Carlo
simulation.Comment: 12 pages, including 2 figure
Expression of Xenobiotic Metabolizing Enzymes in Different Lung Compartments of Smokers and Nonsmokers
BACKGROUND: Cytochrome P450 monooxygenases (CYP) play an important role in the defense against inhaled toxicants, and expression of CYP enzymes may differ among various lung cells and tissue compartments. METHODS: We studied the effects of tobacco smoke in volunteers and investigated gene expression of 19 CYPs and 3 flavin-containing monooxygenases, as well as isoforms of gluthathione S-transferases (GST) and uridine diphosphate glucuronosyltransferases (UGT) and the microsomal epoxide hydrolase (EPHX1) in bronchoalveolar lavage cells and bronchial biopsies derived from smokers (n = 8) and nonsmokers (n = 10). We also investigated gene expression of nuclear transcription factors known to be involved in the regulation of xenobiotic metabolism enzymes. RESULTS: Gene expression of CYP1A1, CYP1B1, CYP2S1, GSTP1, and EPHX1 was induced in bronchoalveolar lavage cells of smokers, whereas expression of CYP2B6/7, CYP3A5, and UGT2A1 was repressed. In bronchial biopsies of smokers, CYP1A1, CYP1B1, CYP2C9, GSTP1, and GSTA2 were induced, but CYP2J2 and EPHX1 were repressed. Induction of CYP1A1 and CYP1B1 transcript abundance resulted in increased activity of the coded enzyme. Finally, expression of the liver X receptor and the glucocorticoid receptor was significantly up-regulated in bronchoalveolar lavage cells of smokers. CONCLUSIONS: We found gene expression of pulmonary xenobiotic metabolizing enzymes and certain key transcription factors to be regulated in bronchoalveolar lavage cells and bronchial biopsies of smokers. The observed changes demonstrate tissue specificity in xenobiotic metabolism, with likely implications for the metabolic activation of procarcinogens to ultimate carcinogens of tobacco smoke
Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (cox1, nad1) Gene Sequence Data
The systematics of the poriferan Order Haplosclerida (Class Demospongiae) has been under scrutiny for a number of years without resolution. Molecular data suggests that the order needs revision at all taxonomic levels. Here, we provide a comprehensive view of the phylogenetic relationships of the marine Haplosclerida using many species from across the order, and three gene regions. Gene trees generated using 28S rRNA, nad1 and cox1 gene data, under maximum likelihood and Bayesian approaches, are highly congruent and suggest the presence of four clades. Clade A is comprised primarily of species of Haliclona and Callyspongia, and clade B is comprised of H. simulans and H. vansoesti (Family Chalinidae), Amphimedon queenslandica (Family Niphatidae) and Tabulocalyx (Family Phloeodictyidae), Clade C is comprised primarily of members of the Families Petrosiidae and Niphatidae, while Clade D is comprised of Aka species. The polyphletic nature of the suborders, families and genera described in other studies is also found here
A model for the atomic-scale structure of a dense, nonequilibrium fluid: the homogeneous cooling state of granular fluids
It is shown that the equilibrium Generalized Mean Spherical Model of fluid
structure may be extended to nonequilibrium states with equation of state
information used in equilibrium replaced by an exact condition on the two-body
distribution function. The model is applied to the homogeneous cooling state of
granular fluids and upon comparison to molecular dynamics simulations is found
to provide an accurate picture of the pair distribution function.Comment: 29 pages, 11 figures Revision corrects formatting of the figure
- …