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A theoretical equation of state for detonation products
A theoretical equation of state for detonation products is described that places particular emphasis on the characterization of small carbon clusters (20{angstrom}--50{angstrom} in diameter) in the products. Diamond clusters are modeled with the dangling bonds on the surface atoms (up to 30% of the cluster) capped by various radicals composed of C, H, N, and O from the background molecular fluid mixture. Free energy methods for the surface groups are used to determine the chemical equilibrium composition of the cluster surface as well as the surrounding molecular fluid mixture. The surface composition shows dramatic changes in composition over some regions and varies slowly in others. A perturbation theory approach is used for the mixture of molecular fluids that also includes features based on Monte Carlo simulations
Consistent Anisotropic Repulsions for Simple Molecules
We extract atom-atom potentials from the effective spherical potentials that
suc cessfully model Hugoniot experiments on molecular fluids, e.g., and
. In the case of the resulting potentials compare very well with the
atom-atom potentials used in studies of solid-state propertie s, while for
they are considerably softer at short distances. Ground state (T=0K) and
room temperatu re calculations performed with the new potential resolve
the previous discrepancy between experimental and theoretical results.Comment: RevTeX, 5 figure
Investigating genome wide dna methylation in airway smooth muscle cells from asthmatic and non-asthmatic donors
Rationale: Genetic mechanisms fail to fully explain asthma pathogenesis and environmental factors are considered to play an important role. Environmental factors may lead to permanent changes in epigenetic patterns and contribute to asthma. Epigenetics is the study of heritable changes in gene expression that are not due to changes in DNA sequence. DNA methylation is a reversible modification of DNA structure in which a methyl group is added to cytosine residues. Parental smoking affects the methylation of buccal cell DNA from children and children with early onset wheeze have an altered blood DNA methylation profile to healthy individuals. No studies have compared DNA methylation profiles in the disease relevant cell type of airway smooth muscle (ASM) cells.
Methods: DNA was isolated from ASM cells at passage 5 and bisulphite treated to convert epigenetic information into sequence-based information. Site specific, quantitative genome wide methylation was determined using the Illumina 450K Infinium Methylation BeadChip array. Hits were validated by Pyrosequencing. RNA was extracted simultaneously for mRNA expression analysis by real time PCR.
Results: There were no independent CpG sites associated with asthmatic status of ASM cells following multiple test correction. Without correction over 13000 CpG sites showed a significant difference in methylation (linear modelling, p value >0.05) between asthmatic and non-asthmatic cells, and a biologically relevant difference in methylation of greater that 10% (β value >0.1 ). 10 of these sites were selected as top hits. 7 sites positively validated by pyrosequencing. They were associated with 7 different genes; LGALS3BP, ATP11A, ZNF696, KLF6, TBX1, RUNX3, and SPINT2. Expression of these genes was measured in ASM cells isolated from asthmatic and non-asthmatic donors. LGALS3BP expression was undetectable while ATP11A and ZNF696 displayed no difference in expression between cells from asthmatic and non-asthmatic donors. KLF6 and SPINT2 showed a trend towards increased expression in cells from asthmatic donors while RUNX3 and TBX1 showed a trend towards decreased expression.
Conclusions: Differences in CpG methylation exist between ASM isolated from asthmatic and non-asthmatic donors. Future work will focus on identifying differentially methylated regions of DNA and further defining the association to gene and protein expression
Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
Water and water-mediated interactions determine thermodynamic and kinetics of
protein folding, protein aggregation and self-assembly in confined spaces. To
obtain insights into the role of water in the context of folding problems, we
describe computer simulations of a few related model systems. The dynamics of
collapse of eicosane shows that upon expulsion of water the linear hydrocarbon
chain adopts an ordered helical hairpin structure with 1.5 turns. The structure
of dimer of eicosane molecules has two well ordered helical hairpins that are
stacked perpendicular to each other. As a prelude to studying folding in
confined spaces we used simulations to understand changes in hydrophobic and
ionic interactions in nano droplets. Solvation of hydrophobic and charged
species change drastically in nano water droplets. Hydrophobic species are
localized at the boundary. The tendency of ions to be at the boundary where
water density is low increases as the charge density decreases. Interaction
between hydrophobic, polar, and charged residue are also profoundly altered in
confined spaces. Using the results of computer simulations and accounting for
loss of chain entropy upon confinement we argue and then demonstrate, using
simulations in explicit water, that ordered states of generic amphiphilic
peptide sequences should be stabilized in cylindrical nanopores
Transport properties of dense fluid argon
We calculate using molecular dynamics simulations the transport properties of
realistically modeled fluid argon at pressures up to and
temperatures up to . In this context we provide a critique of some newer
theoretical predictions for the diffusion coefficients of liquids and a
discussion of the Enskog theory relevance under two different adaptations:
modified Enskog theory (MET) and effective diameter Enskog theory. We also
analyze a number of experimental data for the thermal conductivity of
monoatomic and small diatomic dense fluids.Comment: 8 pages, 6 figure
Twenty five years after KLS: A celebration of non-equilibrium statistical mechanics
When Lenz proposed a simple model for phase transitions in magnetism, he
couldn't have imagined that the "Ising model" was to become a jewel in field of
equilibrium statistical mechanics. Its role spans the spectrum, from a good
pedagogical example to a universality class in critical phenomena. A quarter
century ago, Katz, Lebowitz and Spohn found a similar treasure. By introducing
a seemingly trivial modification to the Ising lattice gas, they took it into
the vast realms of non-equilibrium statistical mechanics. An abundant variety
of unexpected behavior emerged and caught many of us by surprise. We present a
brief review of some of the new insights garnered and some of the outstanding
puzzles, as well as speculate on the model's role in the future of
non-equilibrium statistical physics.Comment: 3 figures. Proceedings of 100th Statistical Mechanics Meeting,
Rutgers, NJ (December, 2008
NMR and NQR Fluctuation Effects in Layered Superconductors
We study the effect of thermal fluctuations of the s-wave order parameter of
a quasi two dimensional superconductor on the nuclear spin relaxation rate near
the transition temperature Tc. We consider both the effects of the amplitude
fluctuations and the Berezinskii-Kosterlitz-Thouless (BKT) phase fluctuations
in weakly coupled layered superconductors. In the treatment of the amplitude
fluctuations we employ the Gaussian approximation and evaluate the longitudinal
relaxation rate 1/T1 for a clean s-wave superconductor, with and without pair
breaking effects, using the static pair fluctuation propagator D. The increase
in 1/T1 due to pair breaking in D is overcompensated by the decrease arising
from the single particle Green's functions. The result is a strong effect on
1/T1 for even a small amount of pair breaking. The phase fluctuations are
described in terms of dynamical BKT excitations in the form of pancake
vortex-antivortex (VA) pairs. We calculate the effect of the magnetic field
fluctuations caused by the translational motion of VA excitations on 1/T1 and
on the transverse relaxation rate 1/T2 on both sides of the BKT transitation
temperature T(BKT)<Tc. The results for the NQR relaxation rates depend strongly
on the diffusion constant that governs the motion of free and bound vortices as
well as the annihilation of VA pairs. We discuss the relaxation rates for real
multilayer systems where the diffusion constant can be small and thus increase
the lifetime of a VA pair, leading to an enhancement of the rates. We also
discuss in some detail the experimental feasibility of observing the effects of
amplitude fluctuations in layered s-wave superconductors such as the
dichalcogenides and the effects of phase fluctuations in s- or d-wave
superconductors such as the layered cuprates.Comment: 38 pages, 12 figure
Magnetic Fields, Relativistic Particles, and Shock Waves in Cluster Outskirts
It is only now, with low-frequency radio telescopes, long exposures with
high-resolution X-ray satellites and gamma-ray telescopes, that we are
beginning to learn about the physics in the periphery of galaxy clusters. In
the coming years, Sunyaev-Zeldovich telescopes are going to deliver further
great insights into the plasma physics of these special regions in the
Universe. The last years have already shown tremendous progress with detections
of shocks, estimates of magnetic field strengths and constraints on the
particle acceleration efficiency. X-ray observations have revealed shock fronts
in cluster outskirts which have allowed inferences about the microphysical
structure of shocks fronts in such extreme environments. The best indications
for magnetic fields and relativistic particles in cluster outskirts come from
observations of so-called radio relics, which are megaparsec-sized regions of
radio emission from the edges of galaxy clusters. As these are difficult to
detect due to their low surface brightness, only few of these objects are
known. But they have provided unprecedented evidence for the acceleration of
relativistic particles at shock fronts and the existence of muG strength fields
as far out as the virial radius of clusters. In this review we summarise the
observational and theoretical state of our knowledge of magnetic fields,
relativistic particles and shocks in cluster outskirts.Comment: 34 pages, to be published in Space Science Review
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