Statistical Error in Particle Simulations of Hydrodynamic Phenomena

We present predictions for the statistical error due to finite sampling in the presence of thermal fluctuations in molecular simulation algorithms. Specifically, we establish how these errors depend on Mach number, Knudsen number, number of particles, etc. Expressions for the common hydrodynamic variables of interest such as flow velocity, temperature, density, pressure, shear stress and heat flux are derived using equilibrium statistical mechanics. Both volume-averaged and surface-averaged quantities are considered. Comparisons between theory and computations using direct simulation Monte Carlo for dilute gases, and molecular dynamics for dense fluids, show that the use of equilibrium theory provides accurate results.Comment: 24 pages postscript (including 16 figures

The green-striped forest looper on Vancouver Island

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Quantum Electrical Dipole in Triangular Systems: a Model for Spontaneous Polarity in Metal Clusters

Triangular symmetric molecules with mirror symmetry perpendicular to the 3-fold axis are forbidden to have a fixed electrical dipole moment. However, if the ground state is orbitally degenerate and lacks inversion symmetry, then a ``quantum'' dipole moment does exist. The system of 3 electrons in D_3h symmetry is our example. This system is realized in triatomic molecules like Na_3. Unlike the fixed dipole of a molecule like water, the quantum moment does not point in a fixed direction, but lies in the plane of the molecule and takes quantized values +/- mu_0 along any direction of measurement in the plane. An electric field F in the plane leads to a linear Stark splitting +/- mu_0 F}. We introduce a toy model to study the effect of Jahn-Teller distortions on the quantum dipole moment. We find that the quantum dipole property survives when the dynamic Jahn-Teller effect is included, if the distortion of the molecule is small. Linear Stark splittings are suppressed in low fields by molecular rotation, just as the linear Stark shift of water is suppressed, but will be revealed in moderately large applied fields and low temperatures. Coulomb correlations also give a partial suppression.Comment: 10 pages with 7 figures included; thoroughly revised with a new coauthor; final minor change

Transverse instability and its long-term development for solitary waves of the (2+1)-Boussinesq equation

The stability properties of line solitary wave solutions of the (2+1)-dimensional Boussinesq equation with respect to transverse perturbations and their consequences are considered. A geometric condition arising from a multi-symplectic formulation of this equation gives an explicit relation between the parameters for transverse instability when the transverse wavenumber is small. The Evans function is then computed explicitly, giving the eigenvalues for transverse instability for all transverse wavenumbers. To determine the nonlinear and long time implications of transverse instability, numerical simulations are performed using pseudospectral discretization. The numerics confirm the analytic results, and in all cases studied, transverse instability leads to collapse.Comment: 16 pages, 8 figures; submitted to Phys. Rev.

Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination

Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen

Myelomonocytic Cell Lines in Modeling HIV-1 Infection of the Bone Marrow

Human immunodeficiency virus type 1 (HIV-1), the etiologic agent of acquired immunodeficiency syndrome (AIDS), primarily infects T cells and cells of the monocyte-macrophage lineage. This is due to the presence of the cell surface receptor CD4 and the coreceptors, CXCR4, and CCR5. While the T-cell has classically been the cell type associated with HIV-1 disease progression, cells of the monocyte-macrophage lineage have also been shown to play a major role in this viral pathologic process. Classically, this has involved monocytic cells in the peripheral blood and tissue macrophages, however, over the course of HIV disease, the promyelomonocytic cells of the bone marrow (BM) have also been shown to play a role in pathogenesis retroviral disease in that they play an integral role in the reseeding of the periphery and end-organ tissues. This has involved an initial infection of the bone marrow hematopoietic progenitor cells. Given this observation, over the years there have been a number of cell lines that have been developed and provided valuable insights into research questions surrounding HIV-1 infection of the monocyte-macrophage cell lineage. In this regard, we will examine the biological and immunological properties of these BM-derived cell lines with respect to their utility in exploring the pathogenesis of HIV-1 in humans

Gravitational wave bursts from cusps and kinks on cosmic strings

The strong beams of high-frequency gravitational waves (GW) emitted by cusps and kinks of cosmic strings are studied in detail. As a consequence of these beams, the stochastic ensemble of GW's generated by a cosmological network of oscillating loops is strongly non Gaussian, and includes occasional sharp bursts that stand above the ``confusion'' GW noise made of many smaller overlapping bursts. Even if only 10% of all string loops have cusps these bursts might be detectable by the planned GW detectors LIGO/VIRGO and LISA for string tensions as small as $G \mu \sim 10^{-13}$. In the implausible case where the average cusp number per loop oscillation is extremely small, the smaller bursts emitted by the ubiquitous kinks will be detectable by LISA for string tensions as small as $G \mu \sim 10^{-12}$. We show that the strongly non Gaussian nature of the stochastic GW's generated by strings modifies the usual derivation of constraints on $G \mu$ from pulsar timing experiments. In particular the usually considered ``rms GW background'' is, when G \mu \gaq 10^{-7}, an overestimate of the more relevant confusion GW noise because it includes rare, intense bursts. The consideration of the confusion GW noise suggests that a Grand Unified Theory (GUT) value $G \mu \sim 10^{-6}$ is compatible with existing pulsar data, and that a modest improvement in pulsar timing accuracy could detect the confusion noise coming from a network of cuspy string loops down to $G \mu \sim 10^{-11}$. The GW bursts discussed here might be accompanied by Gamma Ray Bursts.Comment: 24 pages, 3 figures, Revtex, submitted to Phys. Rev.

Interface pinning and slow ordering kinetics on infinitely ramified fractal structures

We investigate the time dependent Ginzburg-Landau (TDGL) equation for a non conserved order parameter on an infinitely ramified (deterministic) fractal lattice employing two alternative methods: the auxiliary field approach and a numerical method of integration of the equations of evolution. In the first case the domain size evolves with time as $L(t)\sim t^{1/d_w}$, where $d_w$ is the anomalous random walk exponent associated with the fractal and differs from the normal value 2, which characterizes all Euclidean lattices. Such a power law growth is identical to the one observed in the study of the spherical model on the same lattice, but fails to describe the asymptotic behavior of the numerical solutions of the TDGL equation for a scalar order parameter. In fact, the simulations performed on a two dimensional Sierpinski Carpet indicate that, after an initial stage dominated by a curvature reduction mechanism \`a la Allen-Cahn, the system enters in a regime where the domain walls between competing phases are pinned by lattice defects. The lack of translational invariance determines a rough free energy landscape, the existence of many metastable minima and the suppression of the marginally stable modes, which in translationally invariant systems lead to power law growth and self similar patterns. On fractal structures as the temperature vanishes the evolution is frozen, since only thermally activated processes can sustain the growth of pinned domains.Comment: 16 pages+14 figure

Discovery of optically faint obscured quasars with Virtual Observatory tools

We use Virtual Observatory (VO) tools to identify optically faint, obscured (i.e., type 2) active galactic nuclei (AGN) in the two Great Observatories Origins Deep Survey (GOODS) fields. By employing publicly available X-ray and optical data and catalogues we discover 68 type 2 AGN candidates. The X-ray powers of these sources are estimated by using a previously known correlation between X-ray luminosity and X-ray-to-optical flux ratio. Thirty-one of our candidates have high estimated powers (Lx > 10^44 erg/s) and therefore qualify as optically obscured quasars, the so-called ``QSO 2''. Based on the derived X-ray powers, our candidates are likely to be at relatively high redshifts, z ~ 3, with the QSO 2 at z ~ 4. By going ~ 3 magnitudes fainter than previously known type 2 AGN in the two GOODS fields we are sampling a region of redshift - power space which was previously unreachable with classical methods. Our method brings to 40 the number of QSO 2 in the GOODS fields, an improvement of a factor ~ 4 when compared to the only 9 such sources previously known. We derive a QSO 2 surface density down to 10^-15 erg/cm^2/s in the 0.5 - 8 keV band of >~ 330/deg^2, ~ 30% of which is made up of previously known sources. This is larger than current estimates and some predictions and suggests that the surface density of QSO 2 at faint flux limits has been underestimated. This work demonstrates that VO tools are mature enough to produce cutting-edge science results by exploiting astronomical data beyond ``classical'' identification limits (R <~ 25) with interoperable tools for statistical identification of sources using multiwavelength information.Comment: 16 pages, 6 figures, accepted for publication in Astronomy & Astrophysics. PDF file with higher resolution figures available at http://www.eso.org/~ppadovan/AVO-paper.pd