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 $\cos 2 \phi$ distribution in unpolarized Drell-Yan lepton pair production $p p$ and $p \bar p \to \ell^+ \ell^- X$, without suppression. The asymmetry is expressed as a product of chiral-odd distributions $h_1^\perp(x_1,\bm{p}_\perp^2)\times \bar h_1^\perp(x_2,\bm{k}_\perp^2)$, where the quark-transversity function $h_1^\perp(x,\bm{p}_\perp^2)$ is the transverse momentum dependent, light-cone momentum distribution of transversely polarized quarks in an {\it unpolarized} proton. We compute this (naive) $T$-odd and chiral-odd distribution function and the resulting $\cos 2 \phi$ asymmetry explicitly in a quark-scalar diquark model for the proton with initial-state gluon interaction. In this model the function $h_1^\perp(x,\bm{p}_\perp^2)$ equals the $T$-odd (chiral-even) Sivers effect function $f^\perp_{1T}(x,\bm{p}_\perp^2)$. This suggests that the single-spin asymmetries in the SIDIS and the Drell-Yan process are closely related to the $\cos 2 \phi$ 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