N-Body Simulations of Alternate Gravity Models

Theories in which gravity is weaker on cosmological scales have been proposed to explain the observed acceleration of the universe. The nonlinear regime in such theories is not well studied, though it is likely that observational tests of structure formation will lie in this regime. A class of alternate gravity theories may be approximated by modifying Poisson's equation. We have run N-body simulations of a set of such models to study the nonlinear clustering of matter on 1-100 Mpc scales. We find that nonlinear gravity enhances the deviations of the power spectrum of these models from standard gravity. This occurs due to mode-coupling, so that models with an excess or deficit of large-scale power (at k < 0.2/Mpc) lead to deviations in the power spectrum at smaller scales as well (up to k ~ 1/Mpc), even though the linear spectra match very closely on the smaller scales. This makes it easier to distinguish such models from general relativity using the three-dimensional power spectrum probed by galaxy surveys and the weak lensing power spectrum. If the potential for light deflection is modified in the same way as the potential that affects the dark matter, then weak lensing constrains deviations from gravity even more strongly. Our simulations show that even with a modified potential, gravitational evolution is approximately universal. Based on this, the Peacock-Dodds approach can be adapted to get an analytical fit for the nonlinear power spectra of alternate gravity models, though the recent Smith et al formula is less successful. Our conclusions extend to models with modifications of gravity on scales of 1-20 Mpc. We also use a way of measuring projected power spectra from simulations that lowers the sample variance, so that fewer realizations are needed to reach a desired level of accuracy.Comment: 26 pages, 10 figures, matches published versio

Quantifying Florida Bay Habitat Suitability for Fishes and Invertebrates Under Climate Change Scenarios

The Florida Bay ecosystem supports a number of economically important ecosystem services, including several recreational fisheries, which may be affected by changing salinity and temperature due toclimate change. In this paper, we use a combination of physical models and habitat suitability index models to quantify the effects of potential climate change scenarios on a variety of juvenile fish and lobster species in Florida Bay. The climate scenarios include alterations in sea level, evaporation and precipitation rates, coastal runoff, and water temperature. We find that the changes in habitat suitability vary in both magnitude and direction across the scenarios and species, but are on average small. Only one of the seven species we investigate (Lagodon rhomboides, i.e., pinfish) sees a sizable decrease in optimal habitat under any of the scenarios. This suggests that the estuarine fauna of Florida Bay may not be as vulnerable to climate change as other components of the ecosystem, such as those in the marine/terrestrial ecotone. However, these models are relatively simplistic, looking only at single species effects of physical drivers without considering the many interspecific interactions that may play a key role in the adjustment of the ecosystem as a whole. More complex models that capture the mechanistic links between physics and biology, as well as the complex dynamics of the estuarine food web, may be necessary to further understand the potential effects of climate change on the Florida Bay ecosystem

Spherical Collapse and Cluster Counts in Modified Gravity Models

Modifications to the gravitational potential affect the nonlinear gravitational evolution of large scale structures in the Universe. To illustrate some generic features of such changes, we study the evolution of spherically symmetric perturbations when the modification is of Yukawa type; this is non-trivial, because we should not and do not assume that Birkhoff's theorem applies. We then show how to estimate the abundance of virialized objects in such models. Comparison with numerical simulations shows reasonable agreement: When normalized to have the same fluctuations at early times, weaker large scale gravity produces fewer massive halos. However, the opposite can be true for models that are normalized to have the same linear theory power spectrum today, so the abundance of rich clusters potentially places interesting constraints on such models. Our analysis also indicates that the formation histories and abundances of sufficiently low mass objects are unchanged from standard gravity. This explains why simulations have found that the nonlinear power-spectrum at large k is unaffected by such modifications to the gravitational potential. In addition, the most massive objects in CMB-normalized models with weaker gravity are expected to be similar to the high-redshift progenitors of the most massive objects in models with stronger gravity. Thus, the difference between the cluster and field galaxy populations is expected to be larger in models with stronger large-scale gravity.Comment: 9 pages, 8 figures Accepted by Phys. Rev.

PhyleasProg: a user-oriented web server for wide evolutionary analyses

Evolutionary analyses of biological data are becoming a prerequisite in many fields of biology. At a time of high-throughput data analysis, phylogenetics is often a necessary complementary tool for biologists to understand, compare and identify the functions of sequences. But available bioinformatics tools are frequently not easy for non-specialists to use. We developed PhyleasProg (http://phyleasprog.inra.fr), a user-friendly web server as a turnkey tool dedicated to evolutionary analyses. PhyleasProg can help biologists with little experience in evolutionary methodologies by analysing their data in a simple and robust way, using methods corresponding to robust standards. Via a very intuitive web interface, users only need to enter a list of Ensembl protein IDs and a list of species as inputs. After dynamic computations, users have access to phylogenetic trees, positive/purifying selection data (on site and branch-site models), with a display of these results on the protein sequence and on a 3D structure model, and the synteny environment of related genes. This connection between different domains of phylogenetics opens the way to new biological analyses for the discovery of the function and structure of proteins

BLAST Observations of the South Ecliptic Pole field: Number Counts and Source Catalogs

We present results from a survey carried out by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST) on a 9 deg^2 field near the South Ecliptic Pole at 250, 350 and 500 {\mu}m. The median 1{\sigma} depths of the maps are 36.0, 26.4 and 18.4 mJy, respectively. We apply a statistical method to estimate submillimeter galaxy number counts and find that they are in agreement with other measurements made with the same instrument and with the more recent results from Herschel/SPIRE. Thanks to the large field observed, the new measurements give additional constraints on the bright end of the counts. We identify 132, 89 and 61 sources with S/N>4 at 250, 350, 500 {\mu}m, respectively and provide a multi-wavelength combined catalog of 232 sources with a significance >4{\sigma} in at least one BLAST band. The new BLAST maps and catalogs are available publicly at http://blastexperiment.info.Comment: 25 pages, 6 figures, 4 tables, Accepted by ApJS. Maps and catalogs available at http://blastexperiment.info

Crossing the Phantom Divide: Theoretical Implications and Observational Status

If the dark energy equation of state parameter w(z) crosses the phantom divide line w=-1 (or equivalently if the expression d(H^2(z))/dz - 3\Omega_m H_0^2 (1+z)^2 changes sign) at recent redshifts, then there are two possible cosmological implications: Either the dark energy consists of multiple components with at least one non-canonical phantom component or general relativity needs to be extended to a more general theory on cosmological scales. The former possibility requires the existence of a phantom component which has been shown to suffer from serious theoretical problems and instabilities. Therefore, the later possibility is the simplest realistic theoretical framework in which such a crossing can be realized. After providing a pedagogical description of various dark energy observational probes, we use a set of such probes (including the Gold SnIa sample, the first year SNLS dataset, the 3-year WMAP CMB shift parameter, the SDSS baryon acoustic oscillations peak (BAO), the X-ray gas mass fraction in clusters and the linear growth rate of perturbations at z=0.15 as obtained from the 2dF galaxy redshift survey) to investigate the priors required for cosmological observations to favor crossing of the phantom divide. We find that a low \Omega_m prior (0.2<\Omega_m <0.25) leads, for most observational probes (except of the SNLS data), to an increased probability (mild trend) for phantom divide crossing. An interesting degeneracy of the ISW effect in the CMB perturbation spectrum is also pointed out.Comment: Accepted in JCAP (to appear). Comments added, typos corrected. 19 pages (revtex), 8 figures. The numerical analysis files (Mathematica + Fortran) with instructions are available at http://leandros.physics.uoi.gr/pdl-cross/pdl-cross.htm . The ppt file of a relevant talk may be downloaded from http://leandros.physics.uoi.gr/pdl-cross/pdl2006.pp

Can Early Dark Energy be Detected in Non-Linear Structure?

We present the first study of early dark energy cosmologies using N-body simulations to investigate the formation of non-linear structure. In contrast to expectations from semi-analytic approaches, we find that early dark energy does not imprint a unique signature on the statistics of non-linear structures. Investigating the non-linear power spectra and halo mass functions, we show that universal mass functions hold for early dark energy, making its presence difficult to distinguish from $\Lambda$CDM. Since early dark energy biases the baryon acoustic oscillation scale, the lack of discriminating power is problematic.Comment: 11 pages, 19 figures. Minor changes to match version accepted to MNRA

f(R) theories

Over the past decade, f(R) theories have been extensively studied as one of the simplest modifications to General Relativity. In this article we review various applications of f(R) theories to cosmology and gravity - such as inflation, dark energy, local gravity constraints, cosmological perturbations, and spherically symmetric solutions in weak and strong gravitational backgrounds. We present a number of ways to distinguish those theories from General Relativity observationally and experimentally. We also discuss the extension to other modified gravity theories such as Brans-Dicke theory and Gauss-Bonnet gravity, and address models that can satisfy both cosmological and local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in Relativity, Published version, Comments are welcom

Spitzer MIPS 24 and 70 micron Imaging near the South Ecliptic Pole: Maps and Source Catalogs

We have imaged an 11.5 sq. deg. region of sky towards the South Ecliptic Pole (RA = 04h43m, Dec = -53d40m, J2000) at 24 and 70 microns with MIPS, the Multiband Imaging Photometer for Spitzer. This region is coincident with a field mapped at longer wavelengths by AKARI and the Balloon-borne Large Aperture Submillimeter Telescope. We discuss our data reduction and source extraction procedures. The median depths of the maps are 47 microJy/beam at 24 micron and 4.3 mJy/beam at 70 micron. At 24 micron, we identify 93098 point sources with signal-to-noise ratio (SNR) >5, and an additional 63 resolved galaxies; at 70 micron, we identify 891 point sources with SNR >6. From simulations, we determine a false detection rate of 1.8% (1.1%) for the 24 micron (70 micron) catalog. The 24 and 70 micron point-source catalogs are 80% complete at 230 microJy and 11 mJy, respectively. These mosaic images and source catalogs will be available to the public through the NASA/IPAC Infrared Science Archive.Comment: 30 pages, 9 figures, 4 tables. Submitted to ApJS. Maps and catalogs can be downloaded from http://blastexperiment.info/release/SEP_MIPS/sep-mips.php, and will be soon be available through IRS

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution