523 research outputs found
A Hybrid Monte Carlo Method for Surface Growth Simulations
We introduce an algorithm for treating growth on surfaces which combines
important features of continuum methods (such as the level-set method) and
Kinetic Monte Carlo (KMC) simulations. We treat the motion of adatoms in
continuum theory, but attach them to islands one atom at a time. The technique
is borrowed from the Dielectric Breakdown Model. Our method allows us to give a
realistic account of fluctuations in island shape, which is lacking in
deterministic continuum treatments and which is an important physical effect.
Our method should be most important for problems close to equilibrium where KMC
becomes impractically slow.Comment: 4 pages, 5 figure
Five new genes are important for common polysaccharide antigen biosynthesis in <em>Pseudomonas aeruginosa</em>
ABSTRACT Common polysaccharide antigen (CPA) is a conserved cell surface polysaccharide produced by Pseudomonas aeruginosa. It contains a rhamnan homopolymer and is one of the two forms of O polysaccharide attached to P. aeruginosa lipopolysaccharide (LPS). Our laboratory has previously characterized an eight-gene cluster (pa5447-pa5454 in P. aeruginosa PAO1) required for biosynthesis of CPA. Here we demonstrate that an adjacent five-gene cluster pa5455-pa5459 is also involved. Using reverse transcriptase PCR (RT-PCR), we showed that the original eight-gene cluster and the new five-gene cluster are both organized as operons. We have analyzed the LPS phenotypes of in-frame deletion mutants made in each of the five genes, and the results verified that these five genes are indeed required for CPA biosynthesis, extending the CPA biosynthesis locus to contain 13 contiguous genes. By performing overexpression experiments of different sets of these biosynthesis genes, we were able to obtain information about their possible functions in CPA biosynthesis. IMPORTANCE Lipopolysaccharide (LPS) is an important cell surface structure of Gram-negative bacteria. The human opportunistic pathogen Pseudomonas aeruginosa simultaneously produces an O-antigen-specific (OSA) form and a common polysaccharide antigen (CPA) form of LPS. CPA, the focus of this study, is composed of α-1-2, α1-3-linked d-rhamnose sugars and has been shown to be important for attachment of the bacteria to human airway epithelial cells. Genome sequencing of this species revealed a new five-gene cluster that we predicted to be involved in CPA biosynthesis and modification. In this study, we have generated chromosomal knockouts by performing in-frame deletions and allelic replacements. Characterizing the function of each of the five genes is important for us to better understand CPA biosynthesis and the mechanisms of chain length termination and regulation of this unique D-rhamnan polysaccharide
Metal-insulator transition in disordered 2DEG including temperature effects
We calculate self-consistently the mutual dependence of electron correlations
and electron-defect scattering for a two dimensional electron gas at finite
temperature. We employ an STLS approach to calculate the electron correlations
while the electron scattering rate off Coulombic impurities and surface
roughness is calculated using self-consistent current-relaxation theory. The
methods are combined and self-consistently solved. We discuss a metal-insulator
transition for a range of disorder levels and electron densities. Our results
are in good agreement with recent experimental observations.Comment: 4 pages, RevTeX + epsf, 5 figure
Viscous fingering in liquid crystals: Anisotropy and morphological transitions
We show that a minimal model for viscous fingering with a nematic liquid
crystal in which anisotropy is considered to enter through two different
viscosities in two perpendicular directions can be mapped to a two-fold
anisotropy in the surface tension. We numerically integrate the dynamics of the
resulting problem with the phase-field approach to find and characterize a
transition between tip-splitting and side-branching as a function of both
anisotropy and dimensionless surface tension. This anisotropy dependence could
explain the experimentally observed (reentrant) transition as temperature and
applied pressure are varied. Our observations are also consistent with previous
experimental evidence in viscous fingering within an etched cell and
simulations of solidification.Comment: 12 pages, 3 figures. Submitted to PR
Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines
BMC Medical Genomics4
The aminobisphosphonate pamidronate controls influenza pathogenesis by expanding a γδ T cell population in humanized mice
As shown in humanized mice, a population of Vγ9Vδ2 T cells can reduce the severity and mortality of disease caused by infection with human and avian influenza viruses
Applications of patching to quadratic forms and central simple algebras
This paper provides applications of patching to quadratic forms and central
simple algebras over function fields of curves over henselian valued fields. In
particular, we use a patching approach to reprove and generalize a recent
result of Parimala and Suresh on the u-invariant of p-adic function fields, for
p odd. The strategy relies on a local-global principle for homogeneous spaces
for rational algebraic groups, combined with local computations.Comment: 48 pages; connectivity now required in the definition of rational
group; beginning of Section 4 reorganized; other minor change
Demonstrating various quantum effects with two entangled laser beams
We report on the preparation of entangled two mode squeezed states of yet
unseen quality. Based on a measurement of the covariance matrix we found a
violation of the Reid and Drummond EPR-criterion at a value of only 0.36\pm0.03
compared to the threshold of 1. Furthermore, quantum state tomography was used
to extract a single photon Fock state solely based on homodyne detection,
demonstrating the strong quantum features of this pair of laser-beams. The
probability for a single photon in this ensemble measurement exceeded 2/3
Emulation of a chemical transport model to assess air quality under future emission scenarios for the southwest of Western Australia
Simulation outputs from chemical transport models (CTMs) are essential to plan effective air quality policies. A key strength of these models is their ability to separate out source-specific components which facilitate the simulation of the potential impact of policy on future air quality. However, configuring and running these models is complex and computationally intensive, making the evaluation of multiple scenarios less accessible to many researchers and policy experts. The aim of this work is to present how Gaussian process emulation can provide a top-down approach to interrogating and interpreting the outputs from CTMs at minimal computational cost. A case study is presented (based on fine particle sources in the southwest of Western Australia) to illustrate how an emulator can be constructed to simultaneously evaluate changes in emissions from on-road transport and electricity sectors. This study demonstrates how emulation provides a flexible way of exploring local impacts of electric vehicles and wider regional effects of emissions from electricity generation. The potential for emulators to be applied to other settings involving air quality research is discussed
Initial-State Interactions in the Unpolarized Drell-Yan Process
We show that initial-state interactions contribute to the
distribution in unpolarized Drell-Yan lepton pair production and , without suppression. The asymmetry is expressed as a
product of chiral-odd distributions , where the quark-transversity function
is the transverse momentum dependent, light-cone
momentum distribution of transversely polarized quarks in an {\it unpolarized}
proton. We compute this (naive) -odd and chiral-odd distribution function
and the resulting asymmetry explicitly in a quark-scalar diquark
model for the proton with initial-state gluon interaction. In this model the
function equals the -odd (chiral-even) Sivers
effect function . This suggests that the
single-spin asymmetries in the SIDIS and the Drell-Yan process are closely
related to the asymmetry of the unpolarized Drell-Yan process,
since all can arise from the same underlying mechanism. This provides new
insight regarding the role of quark and gluon orbital angular momentum as well
as that of initial- and final-state gluon exchange interactions in hard QCD
processes.Comment: 22 pages, 6 figure
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