Large-Scale Simulations of Reionization

We use cosmological simulations to explore the large-scale effects of reionization. Since reionization is a process that involves a large dynamic range - from galaxies to rare bright quasars - we need to be able to cover a significant volume of the universe in our simulation without losing hte important small scale effects from galaxies. Here we have taken an approach that uses clumping factors derived from small scale simulations to approximate the radiative transfer on the sub-cell scales. Using this technique, we can cover a simulation size up to $1280 h^{-1} Mpc$ with $10 h^{-1} Mpc$ cells. This allows us to construct synthetic spectra of quasars similar to observed spectra of SDSS quasars at high reshifts and compare them to the observational data. These spectra can then be analyzed for HII region sizes, the presence of the Gunn-Peterson trough and the Lyman-$\alpha$ forest.Comment: 25 page

Large-Scale Simulations of Clusters of Galaxies

We discuss some of the computational challenges encountered in simulating the evolution of clusters of galaxies. Eulerian adaptive mesh refinement (AMR) techniques can successfully address these challenges but are currently being used by only a few groups. We describe our publicly available AMR code, FLASH, which uses an object-oriented framework to manage its AMR library, physics modules, and automated verification. We outline the development of the FLASH framework to include collisionless particles, permitting it to be used for cluster simulation.Comment: 3 pages, 3 figures, to appear in Proceedings of the VII International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2000), Fermilab, Oct. 16-20, 200

The Alignment of Clusters using Large Scale Simulations

The alignment of clusters of galaxies with their nearest neighbours and between clusters within a supercluster is investigated using simulations of 512^{3} dark matter particles for \LambdaCDM and \tauCDM cosmological models. Strongly significant alignments are found for separations of up to 15h^{-1}Mpc in both cosmologies, but for the \LambdaCDM model the alignments extend up to separations of 30h^{-1}Mpc. The effect is strongest for nearest neighbours, but is not significant enough to be useful as an observational discriminant between cosmologies. As a check of whether this difference in alignments is present in other cosmologies, smaller simulations with 256^{3} particles are investigated for 4 different cosmological models. Because of poor number statistics, only the standard CDM model shows indications of having different alignments from the other models.Comment: 6 pages, 5 figures Submitted to MNRA

Large scale simulations of the jet-IGM interaction

In a parameter study extending to jet densities of $10^{-5}$ times the ambient one, I have recently shown that light large scale jets start their lives in a spherical bow shock phase. This allows an easy description of the sideways bow shock propagation in that phase. Here, I present new, bipolar, simulations of very light jets in 2.5D and 3D, reaching the observationally relevant scale of $>200$ jet radii. Deviations from the early bow shock propagation law are expected because of various effects. The net effect is, however, shown to remain small. I calculate the X-ray appearance of the shocked cluster gas and compare it to Cygnus A and 3C 317. Rings, bright spots and enhancements inside the radio cocoon may be explained.Comment: 8 pages, 5 figures, ApSS accepted, proceedings of the virtual jets 2003 conference in Dogliani/Italy, v3: funny and unimportant bug corrected, one reference adde

Immersive 4D Interactive Visualization of Large-Scale Simulations

In dense clusters a bewildering variety of interactions between stars can be observed, ranging from simple encounters to collisions and other mass-transfer encounters. With faster and special-purpose computers like GRAPE, the amount of data per simulation is now exceeding 1TB. Visualization of such data has now become a complex 4D data-mining problem, combining space and time, and finding interesting events in these large datasets. We have recently starting using the virtual reality simulator, installed in the Hayden Planetarium in the American Museum for Natural History, to tackle some of these problem. This work (http://www.astro.umd.edu/nemo/amnh/) reports on our first ``observations'', modifications needed for our specific experiments, and perhaps field ideas for other fields in science which can benefit from such immersion. We also discuss how our normal analysis programs can be interfaced with this kind of visualization.Comment: 4 pages, 1 figure, ADASS-X conference proceeding

Solvent-free coarse-grained lipid model for large-scale simulations

A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction between particles. A bilayer structure is formed by orientation-dependent (tilt and bending) potentials. In this model, the membrane properties (bending rigidity, line tension of membrane edge, area compression modulus, lateral diffusion coefficient, and flip-flop rate) can be varied over broad ranges. The stability of the bilayer membrane is investigated via droplet-vesicle transition. The rupture of the bilayer and worm-like micelle formation can be induced by an increase in the spontaneous curvature of the monolayer membrane.Comment: 13 pages, 19 figure

MovieMaker: A Parallel Movie-Making Software for Large Scale Simulations

We have developed a parallel rendering software for scientific visualization of large-scale, three-dimensional, time development simulations. The goal of this software, MovieMaker, is to generate a movie, or a series of visualization images from totally one TB-scale data within one night (or less than 12 hours). The isocontouring, volume rendering, and streamlines are implemented. MovieMaker is a parallel program for the shared memory architecture with dynamic load balancing and overlapped disk I/O.Comment: 3pages, 5figures, submitted to J. Plasma Physcs (special issue for 19th ICNSP

Large-Scale Simulations of the Two-Dimensional Melting of Hard Disks

Large-scale computer simulations involving more than a million particles have been performed to study the melting transition in a two-dimensional hard disk fluid. The van der Waals loop previously observed in the pressure-density relationship of smaller simulations is shown to be an artifact of finite-size effects. Together with a detailed scaling analysis of the bond orientation order, the new results provide compelling evidence for the Halperin-Nelson-Young picture. Scaling analysis of the translational order also yields a lower bound for the melting density that is much higher than previously thought.Comment: 4 pages, 4 figure

Large Scale Simulations of Two-Species Annihilation, A+B->0, with Drift

We present results of computer simulations of the diffusion-limited reaction process A+B->0, on the line, under extreme drift conditions, for lattices of up to 2^{27} sites, and where the process proceeds to completion (no particles left). These enormous simulations are made possible by the renormalized reaction-cell method (RRC). Our results allow us to resolve an existing controversy about the rate of growth of domain sizes, and about corrections to scaling of the concentration decay.Comment: 13 pages, RevTeX, Submitted to Physics Letters