Nonlinear Evolution of the Genus Statistics with Zel'dovich Approximation

Evolution of genus density is calculated from Gaussian initial conditions using Zel'dovich approximation. A new approach is introduced which formulates the desired quantity in a rotationally invariant manner. It is shown that normalized genus density does not depend on the initial spectral shape but is a function of the fluctuation amplitude only.Comment: 21 pages, 6 Postscript figures, LaTe

Phase diagram of a dilute ferromagnet model with antiferromagnetic next-nearest-neighbor interactions

We have studied the spin ordering of a dilute classical Heisenberg model with spin concentration $x$, and with ferromagnetic nearest-neighbor interaction $J_1$ and antiferromagnetic next-nearest-neighbor interaction $J_2$. Magnetic phases at absolute zero temperature $T = 0$ are determined examining the stiffness of the ground state, and those at finite temperatures $T \neq 0$ are determined calculating the Binder parameter $g_L$ and the spin correlation length $\xi_L$. Three ordered phases appear in the $x-T$ phase diagram: (i) the ferromagnetic (FM) phase; (ii) the spin glass (SG) phase; and (iii) the mixed (M) phase of the FM and the SG. Near below the ferromagnetic threshold $x_{\rm F}$, a reentrant SG transition occurs. That is, as the temperature is decreased from a high temperature, the FM phase, the M phase and the SG phase appear successively. The magnetization which grows in the FM phase disappears in the SG phase. The SG phase is suggested to be characterized by ferromagnetic clusters. We conclude, hence, that this model could reproduce experimental phase diagrams of dilute ferromagnets Fe$_x$Au$_{1-x}$ and Eu$_x$Sr$_{1-x}$S.Comment: 9 pages, 23 figure

A Test of the Particle Paradigm in N-Body Simulations

We present results of tests of the evolution of small ``fluid elements'' in cosmological N--body simulations, to examine the validity of their treatment as particles. We find that even very small elements typically collapse along one axis while expanding along another, often to twice or more their initial comoving diameter. This represents a possible problem for high--resolution uses of such simulations.Comment: Uses aasms4.sty; accepted for publication in ApJ Letters. Files available also at ftp://kusmos.phsx.ukans.edu/preprints/ates

Identifying short motifs by means of extreme value analysis

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability can display large fluctuations from one putative binding site to another. Here we use a self-consistent statistical procedure that accounts correctly for the large deviations of the matching probability to predict the location of short binding sites. We apply it in two distinct situations: (a) the detection of the binding sites for three specific transcription factors on a set of 134 estrogen-regulated genes; (b) the identification, in a set of 138 possible transcription factors, of the ones binding a specific set of nine genes. In both instances, experimental findings are reproduced (when available) and the number of false positives is significantly reduced with respect to the other methods commonly employed.Comment: 6 pages, 5 figure

The intermittent behavior and hierarchical clustering of the cosmic mass field

The hierarchical clustering model of the cosmic mass field is examined in the context of intermittency. We show that the mass field satisfying the correlation hierarchy $\xi_n\simeq Q_n(\xi_2)^{n-1}$ is intermittent if $\kappa < d$, where $d$ is the dimension of the field, and $\kappa$ is the power-law index of the non-linear power spectrum in the discrete wavelet transform (DWT) representation. We also find that a field with singular clustering can be described by hierarchical clustering models with scale-dependent coefficients $Q_n$ and that this scale-dependence is completely determined by the intermittent exponent and $\kappa$. Moreover, the singular exponents of a field can be calculated by the asymptotic behavior of $Q_n$ when $n$ is large. Applying this result to the transmitted flux of HS1700 Ly$\alpha$ forests, we find that the underlying mass field of the Ly$\alpha$ forests is significantly intermittent. On physical scales less than about 2.0 h$^{-1}$ Mpc, the observed intermittent behavior is qualitatively different from the prediction of the hierarchical clustering with constant $Q_n$. The observations, however, do show the existence of an asymptotic value for the singular exponents. Therefore, the mass field can be described by the hierarchical clustering model with scale-dependent $Q_n$. The singular exponent indicates that the cosmic mass field at redshift $\sim 2$ is weakly singular at least on physical scales as small as 10 h$^{-1}$ kpc.Comment: AAS Latex file, 33 pages,5 figures included, accepted for publication in Ap

Beyond Zel'dovich-Type Approximations in Gravitational Instability Theory --- Pad\'e Prescription in Spheroidal Collapse ---

Among several analytic approximations for the growth of density fluctuations in the expanding Universe, Zel'dovich approximation in Lagrangian coordinate scheme is known to be unusually accurate even in mildly non-linear regime. This approximation is very similar to the Pad\'e approximation in appearance. We first establish, however, that these two are actually different and independent approximations with each other by using a model of spheroidal mass collapse. Then we propose Pad\'e-prescribed Zel'dovich-type approximations and demonstrate, within this model, that they are much accurate than any other known nonlinear approximations.Comment: 4 pages, latex, 3 figures include

Perturbative Analysis of Adaptive Smoothing Methods in Quantifying Large-Scale Structure

Smoothing operation to make continuous density field from observed point-like distribution of galaxies is crucially important for topological or morphological analysis of the large-scale structure, such as, the genus statistics or the area statistics (equivalently the level crossing statistics). It has been pointed out that the adaptive smoothing filters are more efficient tools to resolve cosmic structures than the traditional spatially fixed filters. We study weakly nonlinear effects caused by two representative adaptive methods often used in smoothed hydrodynamical particle (SPH) simulations. Using framework of second-order perturbation theory, we calculate the generalized skewness parameters for the adaptive methods in the case of initially power-law fluctuations. Then we apply the multidimensional Edgeworth expansion method and investigate weakly nonlinear evolution of the genus statistics and the area statistics. Isodensity contour surfaces are often parameterized by the volume fraction of the regions above a given density threshold. We also discuss this parameterization method in perturbative manner.Comment: 42 pages including 9 figure, ApJ 537 in pres

The Topology of Large Scale Structure in the 1.2 Jy IRAS Redshift Survey

We measure the topology (genus) of isodensity contour surfaces in volume limited subsets of the 1.2 Jy IRAS redshift survey, for smoothing scales \lambda=4\hmpc, 7\hmpc, and 12\hmpc. At 12\hmpc, the observed genus curve has a symmetric form similar to that predicted for a Gaussian random field. At the shorter smoothing lengths, the observed genus curve shows a modest shift in the direction of an isolated cluster or ``meatball'' topology. We use mock catalogs drawn from cosmological N-body simulations to investigate the systematic biases that affect topology measurements in samples of this size and to determine the full covariance matrix of the expected random errors. We incorporate the error correlations into our evaluations of theoretical models, obtaining both frequentist assessments of absolute goodness-of-fit and Bayesian assessments of models' relative likelihoods. We compare the observed topology of the 1.2 Jy survey to the predictions of dynamically evolved, unbiased, gravitational instability models that have Gaussian initial conditions. The model with an $n=-1$, power-law initial power spectrum achieves the best overall agreement with the data, though models with a low-density cold dark matter power spectrum and an $n=0$ power-law spectrum are also consistent. The observed topology is inconsistent with an initially Gaussian model that has $n=-2$, and it is strongly inconsistent with a Voronoi foam model, which has a non-Gaussian, bubble topology.Comment: ApJ submitted, 39 pages, LaTeX(aasms4), 12 figures, 1 Tabl

Fundamental Discreteness Limitations of Cosmological N-Body Clustering Simulations

We explore some of the effects that discreteness and two-body scattering may have on N-body simulations with ``realistic'' cosmological initial conditions. We use an identical subset of particles from the initial conditions for a $128^3$ Particle-Mesh (PM) calculation as the initial conditions for a variety P$^3$M and Tree code runs. We investigate the effect of mass resolution (the mean interparticle separation) since most ``high resolution'' codes only have high resolution in gravitational force. The phase-insensitive two--point statistics, such as the power spectrum (autocorrelation) are somewhat affected by these variations, but phase-sensitive statistics show greater differences. Results converge at the mean interparticle separation scale of the lowest mass-resolution code. As more particles are added, but the force resolution is held constant, the P$^3$M and the Tree runs agree more and more strongly with each other and with the PM run which had the same initial conditions. This shows high particle density is necessary for correct time evolution, since many different results cannot all be correct. However, they do not so converge to a PM run which continued the fluctuations to small scales. Our results show that ignoring them is a major source of error on comoving scales of the missing wavelengths. This can be resolved by putting in a high particle density. Since the codes never agree well on scales below the mean comoving interparticle separation, we find little justification for quantitative predictions on this scale. Some measures vary by 50%, but others can be off by a factor of three or more. Our results suggest possible problems with the density of galaxy halos, formation of early generation objects such as QSO absorber clouds, etc.Comment: Revised version to be published in Astrophysical Journal. One figure changed; expanded discussion, more information on code parameters. Latex, 44 pages, including 19 figures. Higher resolution versions of Figures 10-15 available at: ftp://kusmos.phsx.ukans.edu/preprints/nbod