A New Parallel N-body Gravity Solver: TPM

We have developed a gravity solver based on combining the well developed Particle-Mesh (PM) method and TREE methods. It is designed for and has been implemented on parallel computer architectures. The new code can deal with tens of millions of particles on current computers, with the calculation done on a parallel supercomputer or a group of workstations. Typically, the spatial resolution is enhanced by more than a factor of 20 over the pure PM code with mass resolution retained at nearly the PM level. This code runs much faster than a pure TREE code with the same number of particles and maintains almost the same resolution in high density regions. Multiple time step integration has also been implemented with the code, with second order time accuracy. The performance of the code has been checked in several kinds of parallel computer configuration, including IBM SP1, SGI Challenge and a group of workstations, with the speedup of the parallel code on a 32 processor IBM SP2 supercomputer nearly linear (efficiency $\approx 80\%$) in the number of processors. The computation/communication ratio is also very high ($\sim 50$), which means the code spends $95\%$ of its CPU time in computation.Comment: 21 Pages Latex file Figures available from anonymous ftp to astro.princeton.edu under /xu/tpm.ps, POP-57

Hydrodynamic and N-body Schemes On An Unstructured, Adaptive Mesh with Applications to Cosmological Simulations

The theory and application of numerical methods for unstructured meshes have been improved significantly in recent years. Because the grids can be place arbitrarily in space, unstructured meshes can provide much higher spatial resolution than regular meshes. The built-in nature of mesh adaptivity for unstructured meshes gives one way to simulate highly dynamic, hierarchical problems involving both collisionless dark matter and collisional gas dynamics. In this paper, we describe algorithms to construct unstructured meshes from a set of points with periodic boundary conditions through Delaunay triangulation, and algorithms to solve hydrodynamic and N-body problems on an unstructured mesh . A combination of a local transformation algorithm and the traditional Bowyer-Watson algorithm gives an efficient approach to perform Delaunay triangulation. A novel algorithm to solve N-body equations of motion on an unstructured mesh is described. Poisson's equation is solved using the conjugate gradient method. A gas-kinetic scheme based on the BGK model to solve Euler equations is used to evolve the hydrodynamic equations. We apply these algorithms to solve cosmological settings, which involve both dark and baryonic matter. Various cooling and heating processes for primordial baryonic matter are included in the code. The numerical results show that the N-body and hydrodynamic algorithms based on unstructured meshes with mesh refinement are well-suited for hierarchical structure formation problems.Comment: 36 pages, Latex, PS file available http://www.ucolick.org/~xu/paper

The Tree-Particle-Mesh N-body Gravity Solver

The Tree-Particle-Mesh (TPM) N-body algorithm couples the tree algorithm for directly computing forces on particles in an hierarchical grouping scheme with the extremely efficient mesh based PM structured approach. The combined TPM algorithm takes advantage of the fact that gravitational forces are linear functions of the density field. Thus one can use domain decomposition to break down the density field into many separate high density regions containing a significant fraction of the mass but residing in a very small fraction of the total volume. In each of these high density regions the gravitational potential is computed via the tree algorithm supplemented by tidal forces from the external density distribution. For the bulk of the volume, forces are computed via the PM algorithm; timesteps in this PM component are large compared to individually determined timesteps in the tree regions. Since each tree region can be treated independently, the algorithm lends itself to very efficient parallelization using message passing. We have tested the new TPM algorithm (a refinement of that originated by Xu 1995) by comparison with results from Ferrell & Bertschinger's P^3M code and find that, except in small clusters, the TPM results are at least as accurate as those obtained with the well-established P^3M algorithm, while taking significantly less computing time. Production runs of 10^9 particles indicate that the new code has great scientific potential when used with distributed computing resources.Comment: 24 pages including 9 figures, uses aaspp4.sty; revised to match published versio

Effects of Salmonella enterica serovar Enteritidis infection on egg production and the immune response of the laying duck Anas platyrhynchos

Persistent colonization of the avian reproductive tract by Salmonella enterica serovar Enteritidis (SE) negatively affects egg production and contaminates the egg. The immune function of the ovary and oviduct is essential for protection from infection and for the production of wholesome eggs. However, the immune response of laying ducks during SE infection is not well-understood. In this study, ducks (Anas platyrhynchos) were infected with SE and were systematically monitored for fecal shedding during a 13-week period. We also assessed bacterial distribution in the reproductive tract and classified infected ducks as resistant or susceptible based on the presence of tissue lesions and on SE isolation from fecal samples. We found that infected animals had persistent, but intermittent, bacterial shedding that resulted in the induction of carrier ducks. Laying rate and egg quality were also decreased after SE infection (P < 0.05). SE readily colonized the stroma, small follicle, isthmus, and vagina in the reproductive tracts of susceptible ducks. Immunoglobulin (IgA, IgG, IgM) levels were higher in susceptible ducks compared with resistant birds (P < 0.05); T-lymphocyte subpopulations (CD3+, CD4+, CD8+) displayed the opposite trend. qRT-PCR analysis was used to examine expression profiles of immune response genes in the reproductive tract of infected ducks. The analysis revealed that immune genes, including toll-like receptors (TLR2, TLR4-5, TLR15, TLR21), NOD-like receptors (NOD1, NLRX1, NLRP12), avian β-defensins (AvβD4-5, AvβD7, AvβD12), cytokines (IL-6, IL-1β, IFN-γ), and MyD88 were markedly upregulated in the reproductive tracts of SE-infected ducks (all P < 0.05); TLR3, TLR7, NLRC3, NLRC5, and TNF-α were significantly downregulated. These results revealed that SE infection promoted lower egg production and quality, and altered the expression of TLRs, NLRs, AvβDs, and cytokine family genes. These findings provide a basis for further investigation of the physiological and immune mechanisms of SE infection in laying ducks

Morphological, anatomical and histological studies on knob and beak characters of six goose breeds from China

The knob serves as both a sexual indicator of a goose’s maturity and a significant packaging attribute that garners consumer attention. However, studies regarding the morphological, anatomical and histological traits of different breeds and ages on the on knob in goose are lacking. In this study, six breeds with typical goose knob types were selected, and their knob size, morphological, anatomical and histological traits were characterized. The results showed that: Knob was more prominent in gander than in female goose, and the difference was the most obvious in Magang goose. Wanxi white goose and Shitou goose had the largest knob bulge, while Magang goose and Sichuan white goose were smaller. The total knob volume of Wanxi White goose and Shitou goose was significantly higher than that of other breeds, regardless of male or female (p &lt; 0.05). The beak volume of Wanxi White goose and gander was significantly higher than that of other goose breeds (p &lt; 0.05). Furthermore, the observation revealed that the “knob” primarily consisted of skin-derived tissue and bony protrusions. As age advances, the knob of both male and female geese undergoes synchronous development, with the knob of male geese typically surpassing that of their female counterparts during the same period. The growth rate of knob in male goose was the fastest from 70 to 120 days of age, and slowed down from 300 to 500 days of age. The growth rate of knob in female goose was slower than that in male goose. There were essential differences in the composition of Yangzhou goose knob and Magang goose knob. The subcutaneous tissue of Magang goose was rich, and the thickness of epidermis, dermis and various layers was significantly smaller than that of Yangzhou goose (p &lt; 0.05). With the growth of goose knob, the cells of the epidermal spinous layer became denser and gradually condensed into an overall structure, and there was a clear boundary between the dermis and epidermis after adult. In adulthood, the fiber fascicle network was staggered and dense, with greater toughness and elasticity, and the stratum corneum, epidermis, reticular layer, dermis and other skin structural layers became thicker