Sub-mm Galaxies in Cosmological Simulations

We study the predicted sub-mm emission from massive galaxies in a Lambda-CDM universe, using hydrodynamic cosmological simulations. Assuming that most of the emission from newly formed stars is absorbed and reradiated in the rest-frame far-IR, we calculate the number of galaxies that would be detected in sub-mm surveys conducted with SCUBA. The predicted number counts are strongly dependent on the assumed dust temperature and emissivity law. With plausible choices for SED parameters (e.g., T=35 K, beta=1.0), the simulation predictions reproduce the observed number counts above ~ 1 mJy. The sources have a broad redshift distribution with median z ~ 2, in reasonable agreement with observational constraints. However, the predicted count distribution may be too steep at the faint end, and the fraction of low redshift objects may be larger than observed. In this physical model of the sub-mm galaxy population, the objects detected in existing surveys consist mainly of massive galaxies (several M_*) forming stars fairly steadily over timescales ~ 10^8-10^9 years, at moderate rates ~100 Msun/yr. The typical descendants of these sub-mm sources are even more massive galaxies, with old stellar populations, found primarily in dense environments. While the resolution of our simulations is not sufficient to determine galaxy morphologies, these properties support the proposed identification of sub-mm sources with massive ellipticals in the process of formation. The most robust and distinctive prediction of this model, stemming directly from the long timescale and correspondingly moderate rate of star formation, is that the far-IR SEDs of SCUBA sources have a relative high 850 micron luminosity for a given bolometric luminosity. [Abridged]Comment: Submitted to ApJ. 34 pages including 8 PS figure

A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

BACKGROUND: Many of the most popular pre-processing methods for Affymetrix expression arrays, such as RMA, gcRMA, and PLIER, simultaneously analyze data across a set of predetermined arrays to improve precision of the final measures of expression. One problem associated with these algorithms is that expression measurements for a particular sample are highly dependent on the set of samples used for normalization and results obtained by normalization with a different set may not be comparable. A related problem is that an organization producing and/or storing large amounts of data in a sequential fashion will need to either re-run the pre-processing algorithm every time an array is added or store them in batches that are pre-processed together. Furthermore, pre-processing of large numbers of arrays requires loading all the feature-level data into memory which is a difficult task even with modern computers. We utilize a scheme that produces all the information necessary for pre-processing using a very large training set that can be used for summarization of samples outside of the training set. All subsequent pre-processing tasks can be done on an individual array basis. We demonstrate the utility of this approach by defining a new version of the Robust Multi-chip Averaging (RMA) algorithm which we refer to as refRMA. RESULTS: We assess performance based on multiple sets of samples processed over HG U133A Affymetrix GeneChip(® )arrays. We show that the refRMA workflow, when used in conjunction with a large, biologically diverse training set, results in the same general characteristics as that of RMA in its classic form when comparing overall data structure, sample-to-sample correlation, and variation. Further, we demonstrate that the refRMA workflow and reference set can be robustly applied to naïve organ types and to benchmark data where its performance indicates respectable results. CONCLUSION: Our results indicate that a biologically diverse reference database can be used to train a model for estimating probe set intensities of exclusive test sets, while retaining the overall characteristics of the base algorithm. Although the results we present are specific for RMA, similar versions of other multi-array normalization and summarization schemes can be developed

Calculation of Heavy Ion Inactivation and Mutation Rates in Radial Dose Model of Track Structure

In the track structure model, the inactivation cross section is found by summing an inactivation probability over all impact parameters from the ion to the sensitive sites within the cell nucleus. The inactivation probability is evaluated by using the dose response of the system to gamma rays and the radial dose of the ions and may be equal to unity at small impact parameters. We apply the track structure model to recent data with heavy ion beams irradiating biological samples of E. Coli, Bacillus Subtilis spores, and Chinese hamster (V79) cells. Heavy ions have observed cross sections for inactivation that approach and sometimes exceed the geometric size of the cell nucleus in mammalian cells. We show how the effects of inactivation may be taken into account in the evaluation of the mutation cross sections from heavy ions in the track structure model through correlation of sites for gene mutation and cell inactivation. The model is fit to available data for HPRT (hypoxanthine guanine phosphoribosyl transferase) mutations in Chinese hamster cells, and good agreement is found. The resulting calculations qualitatively show that mutation cross sections for heavy ions display minima at velocities where inactivation cross sections display maxima. Also, calculations show the high probability for mutation by relativistic ions due to the radial extension of the ion track from delta rays in agreement with the microlesion concept. The effects of inactivation on mutation rates make it very unlikely that a single parameter such as LET (linear energy transfer) or Z*2/ β2&#;(where Z*is effective charge number and β is ion velocity) can be used to specify radiation quality for heavy ion bombardment

Calculation of Heavy Ion Inactivation and Mutation Rates in Radial Dose Model of Track Structure

In the track structure model, the inactivation cross section is found by summing an inactivation probability over all impact parameters from the ion to the sensitive sites within the cell nucleus. The inactivation probability is evaluated by using the dose response of the system to gamma rays and the radial dose of the ions and may be equal to unity at small impact parameters. We apply the track structure model to recent data with heavy ion beams irradiating biological samples of E. Coli, B. Subtilis spores, and Chinese hamster (V79) cells. Heavy ions have observed cross sections for inactivation that approach and sometimes exceed the geometric size of the cell nucleus. We show how the effects of inactivation may be taken into account in the evaluation of the mutation cross sections in the track structure model through correlation of sites for gene mutation and cell inactivation. The model is fit to available data for HPRT (hypoxanthine guanine phosphoribosyl transferase) mutations in V79 cells, and good agreement is found. Calculations show the high probability for mutation by relativistic ions due to the radial extension of ions track from delta rays. The effects of inactivation on mutation rates make it very unlikely that a single parameter such as LET (linear energy transfer) can be used to specify radiation quality for heavy ion bombardment

Calculation of Heavy Ion Inactivation and Mutation Rates in Radial Dose Model of Track Structure

In the track structure model, the inactivation cross section is found by summing an inactivation probability over all impact parameters from the ion to the sensitive sites within the cell nucleus. The inactivation probability is evaluated by using the dose response of the system to gamma rays and the radial dose of the ions and may be equal to unity at small impact parameters. We apply the track structure model to recent data with heavy ion beams irradiating biological samples of E. Coli, Bacillus Subtilis spores, and Chinese hamster (V79) cells. Heavy ions have observed cross sections for inactivation that approach and sometimes exceed the geometric size of the cell nucleus in mammalian cells. We show how the effects of inactivation may be taken into account in the evaluation of the mutation cross sections from heavy ions in the track structure model through correlation of sites for gene mutation and cell inactivation. The model is fit to available data for HPRT (hypoxanthine guanine phosphoribosyl transferase) mutations in Chinese hamster cells, and good agreement is found. The resulting calculations qualitatively show that mutation cross sections for heavy ions display minima at velocities where inactivation cross sections display maxima. Also, calculations show the high probability for mutation by relativistic ions due to the radial extension of the ion track from delta rays in agreement with the microlesion concept. The effects of inactivation on mutation rates make it very unlikely that a single parameter such as LET (linear energy transfer) or Z*2/ β2&#;(where Z*is effective charge number and β is ion velocity) can be used to specify radiation quality for heavy ion bombardment

Cooling Radiation and the Lyman-alpha Luminosity of Forming Galaxies

We examine the cooling radiation from forming galaxies in hydrodynamic simulations of the LCDM model (cold dark matter with a cosmological constant), focusing on the Ly-alpha line luminosities of high-redshift systems. Primordial composition gas condenses within dark matter potential wells, forming objects with masses and sizes comparable to the luminous regions of observed galaxies. As expected, the energy radiated in this process is comparable to the gravitational binding energy of the baryons, and the total cooling luminosity of the galaxy population peaks at z ~= 2. However, in contrast to the classical picture of gas cooling from the \sim 10^6 K virial temperature of a typical dark matter halo, we find that most of the cooling radiation is emitted by gas with T < 20,000 K. As a consequence, roughly 50% of this cooling radiation emerges in the Ly-alpha line. While a galaxy's cooling luminosity is usually smaller than the ionizing continuum luminosity of its young stars, the two are comparable in the most massive systems, and the cooling radiation is produced at larger radii, where the Ly-alpha photons are less likely to be extinguished by dust. We suggest, in particular, that cooling radiation could explain the two large (\sim 100 kpc), luminous (L_{Ly-alpha} \sim 10^{44} erg s^{-1}) ``blobs'' of Ly-alpha emission found in Steidel et al.'s (1999) narrow band survey of a z = 3 proto-cluster. Our simulations predict objects of the observed luminosity at about the right space density, and radiative transfer effects can account for the observed sizes and line widths. We discuss observable tests of this hypothesis for the nature of the Ly-alpha blobs, and we present predictions for the contribution of cooling radiation to the Ly-alpha luminosity function of galaxies as a function of redshift.Comment: Submitted to ApJ. 28 pages including 9 PS figures. Version with color figures available at http://donald.astro.umass.edu/~fardal/papers/cooling/cooling.htm

Radiation risk predictions for Space Station Freedom orbits

Risk assessment calculations are presented for the preliminary proposed solar minimum and solar maximum orbits for Space Station Freedom (SSF). Integral linear energy transfer (LET) fluence spectra are calculated for the trapped proton and GCR environments. Organ dose calculations are discussed using the computerized anatomical man model. The cellular track model of Katz is applied to calculate cell survival, transformation, and mutation rates for various aluminum shields. Comparisons between relative biological effectiveness (RBE) and quality factor (QF) values for SSF orbits are made

The Photon Underproduction Crisis

We examine the statistics of the low-redshift Lyman-alpha forest from smoothed particle hydrodynamic simulations in light of recent improvements in the estimated evolution of the cosmic ultraviolet background (UVB) and recent observations from the Cosmic Origins Spectrograph (COS). We find that the value of the metagalactic photoionization rate required by our simulations to match the observed properties of the low-redshift Lyman-alpha forest is a factor of 5 larger than the value predicted by state-of-the art models for the evolution of this quantity. This mismatch results in the mean flux decrement of the Lyman-alpha forest being underpredicted by at least a factor of 2 (a 10-sigma discrepancy with observations) and a column density distribution of Lyman-alpha forest absorbers systematically and significantly elevated compared to observations over nearly two decades in column density. We examine potential resolutions to this mismatch and find that either conventional sources of ionizing photons (galaxies and quasars) must be significantly elevated relative to current observational estimates or our theoretical understanding of the low-redshift universe is in need of substantial revision.Comment: Submitted to ApJ Letters; 6 pages including 3 figure

Hydrodynamic Simulation of the Cosmological X-ray Background

(Abridged) We use a hydrodynamic simulation of a LambdaCDM model to predict the extragalactic X-ray background (XRB), focussing on emission from the intergalactic medium (IGM). We also include X-rays from point sources associated with galaxies in the simulation, and make maps of the angular distribution of the emission. We find that filaments in the maps are not evident, being diluted by projection. In the soft (0.5-2 keV) band, the mean intensity of radiation from intergalactic and cluster gas is 2.3*10^-12 ergdeg^-2cm^-2s^-1, 35% of the total soft band emission. This is compatible at the ~1 sigma level with estimates of the unresolved soft background from ROSAT and {\it Chandra}. Only 4% of the hard (2-10 keV) emission is associated with the IGM. Relative to AGN flux, the IGM component peaks at a lower redshift (median z~0.45) so its clustering makes an important contribution to that of the total XRB. The angular correlations on 0.1-10 arcmin scales are significant, with an amplitude roughly consistent with an extrapolation of recent ROSAT results to small scales. A cross-correlation of the XRB against nearby galaxies taken from a simulated redshift survey also yields a strong signal from the IGM. Although some recent papers have argued that the expected soft band intensity from gas in galaxy, group, and cluster halos would exceed XRB limits unless much of the gas is expelled by supernova feedback, we obtain reasonable compatibility with current observations in a simulation that incorporates cooling, star formation, and only modest feedback. A prediction of our model is that the unresolved portion of the soft XRB will remain mostly unresolved.Comment: Improved referencing of related papers. Submitted to ApJ, 19 pages, 17 postscript figures, most reduced in resolution, emulateapj.sty, for full resolution version, see http://cfa-www.harvard.edu/~rcroft/xray.ps.g