FISH: A 3D parallel MHD code for astrophysical applications

FISH is a fast and simple ideal magneto-hydrodynamics code that scales to ~10 000 processes for a Cartesian computational domain of ~1000^3 cells. The simplicity of FISH has been achieved by the rigorous application of the operator splitting technique, while second order accuracy is maintained by the symmetric ordering of the operators. Between directional sweeps, the three-dimensional data is rotated in memory so that the sweep is always performed in a cache-efficient way along the direction of contiguous memory. Hence, the code only requires a one-dimensional description of the conservation equations to be solved. This approach also enable an elegant novel parallelisation of the code that is based on persistent communications with MPI for cubic domain decomposition on machines with distributed memory. This scheme is then combined with an additional OpenMP parallelisation of different sweeps that can take advantage of clusters of shared memory. We document the detailed implementation of a second order TVD advection scheme based on flux reconstruction. The magnetic fields are evolved by a constrained transport scheme. We show that the subtraction of a simple estimate of the hydrostatic gradient from the total gradients can significantly reduce the dissipation of the advection scheme in simulations of gravitationally bound hydrostatic objects. Through its simplicity and efficiency, FISH is as well-suited for hydrodynamics classes as for large-scale astrophysical simulations on high-performance computer clusters. In preparation for the release of a public version, we demonstrate the performance of FISH in a suite of astrophysically orientated test cases.Comment: 27 pages, 11 figure

Power Spectra in Global Defect Theories of Cosmic Structure Formation

An efficient technique for computing perturbation power spectra in field ordering theories of cosmic structure formation is introduced, enabling computations to be carried out with unprecedented precision. Large scale simulations are used to measure unequal time correlators of the source stress energy, taking advantage of scaling during matter and radiation domination, and causality, to make optimal use of the available dynamic range. The correlators are then re-expressed in terms of a sum of eigenvector products, a representation which we argue is optimal, enabling the computation of the final power spectra to be performed at high accuracy. Microwave anisotropy and matter perturbation power spectra for global strings, monopoles, textures and non-topological textures are presented and compared with recent observations.Comment: 4 pages, compressed and uuencoded RevTex file and postscript figure

Particle trajectory computer program for icing analysis of axisymmetric bodies

General aviation aircraft and helicopters exposed to an icing environment can accumulate ice resulting in a sharp increase in drag and reduction of maximum lift causing hazardous flight conditions. NASA Lewis Research Center (LeRC) is conducting a program to examine, with the aid of high-speed computer facilities, how the trajectories of particles contribute to the ice accumulation on airfoils and engine inlets. This study, as part of the NASA/LeRC research program, develops a computer program for the calculation of icing particle trajectories and impingement limits relative to axisymmetric bodies in the leeward-windward symmetry plane. The methodology employed in the current particle trajectory calculation is to integrate the governing equations of particle motion in a flow field computed by the Douglas axisymmetric potential flow program. The three-degrees-of-freedom (horizontal, vertical, and pitch) motion of the particle is considered. The particle is assumed to be acted upon by aerodynamic lift and drag forces, gravitational forces, and for nonspherical particles, aerodynamic moments. The particle momentum equation is integrated to determine the particle trajectory. Derivation of the governing equations and the method of their solution are described in Section 2.0. General features, as well as input/output instructions for the particle trajectory computer program, are described in Section 3.0. The details of the computer program are described in Section 4.0. Examples of the calculation of particle trajectories demonstrating application of the trajectory program to given axisymmetric inlet test cases are presented in Section 5.0. For the examples presented, the particles are treated as spherical water droplets. In Section 6.0, limitations of the program relative to excessive computer time and recommendations in this regard are discussed

Antiviral RNA Interference against Orsay Virus Is neither Systemic nor Transgenerational in Caenorhabditis elegans.

UNLABELLED: Antiviral RNA-mediated silencing (RNA interference [RNAi]) acts as a powerful innate immunity defense in plants, invertebrates, and mammals. In Caenorhabditis elegans, RNAi is systemic; i.e., RNAi silencing signals can move between cells and tissues. Furthermore, RNAi effects can be inherited transgenerationally and may last for many generations. Neither the biological relevance of systemic RNAi nor transgenerational RNAi is currently understood. Here we examined the role of both pathways in the protection of C. elegans from viral infection. We studied the Orsay virus, a positive-strand RNA virus related to Nodaviridae and the first and only virus known to infect C. elegans. Immunity to Orsay virus infection requires the RNAi pathway. Surprisingly, we found that genes required for systemic or transgenerational RNAi did not have a role in antiviral defense. Furthermore, we found that Orsay virus infection did not elicit a systemic RNAi response even when a target for RNAi was provided by using transgenes. Finally, we show that viral siRNAs, the effectors of RNAi, are not inherited to a level that provides any significant resistance to viral infection in the next generation. We conclude that systemic or transgenerational RNAi does not play a role in the defense against natural Orsay virus infection. Furthermore, our data suggest that there is a qualitative difference between experimental RNAi and antiviral RNAi. Our data are consistent with a model of systemic and transgenerational RNAi that requires a nuclear or germ line component that is lacking in almost all RNA virus infections. IMPORTANCE: Since its discovery in Caenorhabditis elegans, RNAi has proven a valuable scientific tool in many organisms. In C. elegans, exogenous RNAi spreads throughout the organism and can be passed between generations; however, there has been controversy as to the endogenous role(s) that the RNAi pathway plays. One endogenous role for which spreading both within the infected organism and between generations would be advantageous is a role in viral defense. In plants, antiviral RNAi is systemic and the spread of RNAi between cells provides protection against subsequent viral infection. Here we investigated this by using the only naturally occurring virus known to infect C. elegans, Orsay virus, and surprisingly found that, in contrast to the exogenous RNAi pathway, the antiviral RNAi response targeted against this virus does not spread systemically throughout the organism and cannot be passed between generations. These results suggest that there are differences between the two pathways that remain to be discovered

Simulating Reionization: Character and Observability

In recent years there has been considerable progress in our understanding of the nature and properties of the reionization process. In particular, the numerical simulations of this epoch have made a qualitative leap forward, reaching sufficiently large scales to derive the characteristic scales of the reionization process and thus allowing for realistic observational predictions. Our group has recently performed the first such large-scale radiative transfer simulations of reionization, run on top of state-of-the-art simulations of early structure formation. This allowed us to make the first realistic observational predictions about the Epoch of Reionization based on detailed radiative transfer and structure formation simulations. We discuss the basic features of reionization derived from our simulations and some recent results on the observational implications for the high-redshift Ly-alpha sources.Comment: 3 pages, to appear in the Proceedings of First Stars III, Santa Fe, July 2007, AIP Conference Serie

Cosmic Microwave Background Anisotropies from Scaling Seeds: Fit to Observational Data

We compute cosmic microwave background angular power spectra for scaling seed models of structure formation. A generic parameterization of the energy momentum tensor of the seeds is employed. We concentrate on two regions of parameter space inspired by global topological defects: O(4) texture models and the large-N limit of O(N) models. We use $\chi^{2}$ fitting to compare these models to recent flat-band power measurements of the cosmic microwave background. Only scalar perturbations are considered.Comment: LaTeX file 4 pages, 4 postscript figs. revised version, to appear in PR

The effect of the intergalactic environment on the observability of Lya emitters during reionization

Observations of high-redshift Lya sources are a major tool for studying the high-redshift universe and are one of the most promising ways to constrain the later stages of reionization. The understanding and interpretation of the data is far from straightforward, however. We discuss the effect of the reionizing intergalactic medium (IGM) on the observability of Lya sources based on large simulations of early structure formation with radiative transfer. This takes into account self-consistently the reionization history, density, velocity and ionization structures and non-linear source clustering. We find that all fields are highly anisotropic and as a consequence there are very large variations in opacity among the different lines of sight. The velocity effects, from both infall and source peculiar velocity are most important for the luminous sources, affecting the line profile and depressing the bright end of the luminosity function. The line profiles are generally asymmetric and the line centres of the luminous sources are always absorbed due to the high density of the local IGM. For both luminous and average sources the damping wing effects are of similar magnitude and remain significant until fairly late, when the IGM is ionized between 30 and 70 per cent by mass

Normalizing the Temperature Function of Clusters of Galaxies

We re-examine the constraints which can be robustly obtained from the observed temperature function of X-ray cluster of galaxies. The cluster mass function has been thoroughly studied in simulations and analytically, but a direct simulation of the temperature function is presented here for the first time. Adaptive hydrodynamic simulations using the cosmological Moving Mesh Hydro code of Pen (1997a) are used to calibrate the temperature function for different popular cosmologies. Applying the new normalizations to the present-day cluster abundances, we find $\sigma_8=0.53\pm 0.05 \Omega_0^{-0.45}$ for a hyperbolic universe, and $\sigma_8=0.53\pm 0.05 \Omega_0^{-0.53}$ for a spatially flat universe with a cosmological constant. The simulations followed the gravitational shock heating of the gas and dark matter, and used a crude model for potential energy injection by supernova heating. The error bars are dominated by uncertainties in the heating/cooling models. We present fitting formulae for the mass-temperature conversions and cluster abundances based on these simulations.Comment: 20 pages incl 5 figures, final version for ApJ, corrected open universe \gamma relation, results unchange