Parallel HOP: A Scalable Halo Finder for Massive Cosmological Data Sets

Modern N-body cosmological simulations contain billions ($10^9$) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory, and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly-employed halo finders, such that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes MPI and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger datasets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit yt, an analysis toolkit for Adaptive Mesh Refinement (AMR) data that includes complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and datasets in excess of $2000^3$ particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable.Comment: 29 pages, 11 figures, 2 table

Face-Specific Resting Functional Connectivity between the Fusiform Gyrus and Posterior Superior Temporal Sulcus

Faces activate specific brain regions in fMRI, including the fusiform gyrus (FG) and the posterior superior temporal sulcus (pSTS). The fact that the FG and pSTS are frequently co-activated suggests that they may interact synergistically in a distributed face processing network. Alternatively, the functions implemented by these regions may be encapsulated from each other. It has proven difficult to evaluate these two accounts during visual processing of face stimuli. However, if the FG and pSTS interact during face processing, the substrate for such interactions may be apparent in a correlation of the BOLD timeseries from these two regions during periods of rest when no faces are present. To examine face-specific resting correlations, we developed a new partial functional connectivity approach in which we removed variance from the FG that was shared with other category-selective and control regions. The remaining face-specific FG resting variance was then used to predict resting signals throughout the brain. In two experiments, we observed face-specific resting functional connectivity between FG and pSTS, and importantly, these correlations overlapped precisely with the face-specific pSTS region obtained from independent localizer runs. Additional region-of-interest and pattern analyses confirmed that the FG–pSTS resting correlations were face-specific. These findings support a model in which face processing is distributed among a finite number of connected, but nevertheless face-specialized regions. The discovery of category-specific interactions in the absence of visual input suggests that resting networks may provide a latent foundation for task processing

The Birth of a Galaxy - III. Propelling reionisation with the faintest galaxies

Starlight from galaxies plays a pivotal role throughout the process of cosmic reionisation. We present the statistics of dwarf galaxy properties at z > 7 in haloes with masses up to 10^9 solar masses, using a cosmological radiation hydrodynamics simulation that follows their buildup starting with their Population III progenitors. We find that metal-enriched star formation is not restricted to atomic cooling ($T_{\rm vir} \ge 10^4$ K) haloes, but can occur in haloes down to masses ~10^6 solar masses, especially in neutral regions. Even though these smallest galaxies only host up to 10^4 solar masses of stars, they provide nearly 30 per cent of the ionising photon budget. We find that the galaxy luminosity function flattens above M_UV ~ -12 with a number density that is unchanged at z < 10. The fraction of ionising radiation escaping into the intergalactic medium is inversely dependent on halo mass, decreasing from 50 to 5 per cent in the mass range $\log M/M_\odot = 7.0-8.5$. Using our galaxy statistics in a semi-analytic reionisation model, we find a Thomson scattering optical depth consistent with the latest Planck results, while still being consistent with the UV emissivity constraints provided by Ly$\alpha$ forest observations at z = 4-6.Comment: 21 pages, 15 figures, 4 tables. Accepted in MNRA

The Biermann Battery in Cosmological MHD Simulations of Population III Star Formation

We report the results of the first self-consistent three-dimensional adaptive mesh refinement magnetohydrodynamical simulations of Population III star formation including the Biermann Battery effect. We find that the Population III stars formed including this effect are both qualitatively and quantitatively similar to those from hydrodynamics-only (non-MHD) cosmological simulations. We observe peak magnetic fields of ~10^-9 G in the center of our star-forming halo at z ~ 17.55. The magnetic fields created by the Biermann Battery effect are predominantly formed early in the evolution of the primordial halo at low density and large spatial scales, and then grow through compression and by shear flows. The fields seen in this calculation are never large enough to be dynamically important (with beta >= 10^{15} at all times), and should be considered the minimum possible fields in existence during Population III star formation, and may be seed fields for the stellar dynamo or the magnetorotational instability at higher densities and smaller spatial scales.Comment: 4 pages, 3 figures; Submitted to the Astrophysical Journal Letters. Comments welcome. Typo found (and fixed) in equation

Open questions in the study of population III star formation

The first stars were key drivers of early cosmic evolution. We review the main physical elements of the current consensus view, positing that the first stars were predominantly very massive. We continue with a discussion of important open questions that confront the standard model. Among them are uncertainties in the atomic and molecular physics of the hydrogen and helium gas, the multiplicity of stars that form in minihalos, and the possible existence of two separate modes of metal-free star formation.Comment: 15 pages, 2 figures. To appear in the conference proceedings for IAU Symposium 255: Low-Metallicity Star Formation: From the First Stars to Dwarf Galaxie

The Santa Fe Light Cone Simulation Project: II. The Prospects for Direct Detection of the WHIM with SZE Surveys

Detection of the Warm-Hot Intergalactic Medium (WHIM) using Sunyaev-Zeldovich effect (SZE) surveys is an intriguing possibility, and one that may allow observers to quantify the amount of "missing baryons" in the WHIM phase. We estimate the necessary sensitivity for detecting low density WHIM gas with the South Pole Telescope (SPT) and Planck Surveyor for a synthetic 100 square degree sky survey. This survey is generated from a very large, high dynamic range adaptive mesh refinement cosmological simulation performed with the Enzo code. We find that for a modest increase in the SPT survey sensitivity (a factor of 2-4), the WHIM gas makes a detectable contribution to the integrated sky signal. For a Planck-like satellite, similar detections are possible with a more significant increase in sensitivity (a factor of 8-10). We point out that for the WHIM gas, the kinematic SZE signal can sometimes dominate the thermal SZE where the thermal SZE decrement is maximal (150 GHz), and that using the combination of the two increases the chance of WHIM detection using SZE surveys. However, we find no evidence of unique features in the thermal SZE angular power spectrum that may aid in its detection. Interestingly, there are differences in the power spectrum of the kinematic SZE, which may not allow us to detect the WHIM directly, but could be an important contaminant in cosmological analyses of the kSZE-derived velocity field. Corrections derived from numerical simulations may be necessary to account for this contamination.Comment: 9 pages, submitted to Astrophysical Journa

Evolution and Distribution of Magnetic Fields from AGNs in Galaxy Clusters. I. The Effect of Injection Energy and Redshift

We present a series of cosmological magnetohydrodynamic (MHD) simulations that simultaneously follow the formation of a galaxy cluster and evolution of magnetic fields ejected by an Active Galactic Nucleus (AGN). Specifically, we investigate the influence of both the epoch of AGN (z $\sim$ 3-0.5) and the AGN energy ($\sim$ 3 $\times$ 10$^{57}$ - 2 $\times$ 10$^{60}$ ergs)on the final magnetic field distribution in a relatively massive cluster (M$_{vir}$ $\sim$10$^{15}$ M$_\odot$). We find that as long as the AGN magnetic fields are ejected before the major mergers in the cluster formation history, magnetic fields can be transported throughout the cluster and can be further amplified by the intra-cluster medium (ICM) turbulence cause by hierarchical mergers during the cluster formation process. The total magnetic energy in the cluster can reach $\sim$ $10^{61}$ ergs, with micro Gauss fields distributed over $\sim$ Mpc scale. The amplification of the total magnetic energy by the ICM turbulence can be significant, up to $\sim$1000 times in some cases. Therefore even weak magnetic fields from AGNs can be used to magnetize the cluster to the observed level. The final magnetic energy in the ICM is determined by the ICM turbulent energy, with a weak dependence on the AGN injection energy. We discuss the properties of magnetic fields throughout the cluster and the synthetic Faraday rotation measure maps they produce. We also show that high spatial resolution over most of the magnetic regions of the cluster is very important to capture the small scale dynamo process and maintain the magnetic field structure in our simulations.Comment: 38 pages, 18 figures, Accepted for publication in Ap

Formation Channels for Population III Stars at Cosmic Dawn

We present a study of the co-evolution of a population of primordial star-forming minihalos at Cosmic Dawn. In this study, we highlight the influence of individual Population III stars on the ability of nearby minihalos to form sufficient molecular hydrogen to undergo star formation of their own. In the absence of radiation, we find the minimum halo mass required to bring about collapse and star formation to be 10^5 Msun, which then increases to 10^6 Msun after two stars have formed. We find an inverse relationship between the mass of a halo and the time required for it to recover its molecular gas after being disrupted by radiation from a nearby star. We also take advantage of the extremely high resolution to investigate the effects of major and minor mergers on the gas content of star-forming minihalos. Contrary to previous claims of fallback of supernova ejecta, we find that minihalos evacuated after hosting Pop III stars primarily recover gas through mergers with undisturbed halos. We identify an intriguing type of major merger between recently evacuated halos and gas-rich ones, finding that these "dry" mergers accelerate star formation instead of suppressing it like their low redshift counterparts. We attribute this to the gas-poor nature of one of the merging halos resulting in no significant rise in temperature or turbulence and instead inducing a rapid increase in central density and hydrostatic pressure. This constitutes a novel formation pathway for Pop III stars and establishes major mergers as potentially the primary source of gas, thus redefining the role of major mergers at this epoch.Comment: 14 pages, 12 figures, submitted to MNRA

The Birth of a Galaxy: Primordial Metal Enrichment and Stellar Populations

By definition, Population III stars are metal-free, and their protostellar collapse is driven by molecular hydrogen cooling in the gas-phase, leading to large characteristic masses. Population II stars with lower characteristic masses form when the star-forming gas reaches a critical metallicity of 10^{-6} - 10^{-3.5} Z_\odot. We present an adaptive mesh refinement radiation hydrodynamics simulation that follows the transition from Population III to II star formation. The maximum spatial resolution of 1 comoving parsec allows for individual molecular clouds to be well-resolved and their stellar associations to be studied in detail. We model stellar radiative feedback with adaptive ray tracing. A top-heavy initial mass function for the Population III stars is considered, resulting in a plausible distribution of pair-instability supernovae and associated metal enrichment. We find that the gas fraction recovers from 5 percent to nearly the cosmic fraction in halos with merger histories rich in halos above 10^7 solar masses. A single pair-instability supernova is sufficient to enrich the host halo to a metallicity floor of 10^{-3} Z_\odot and to transition to Population II star formation. This provides a natural explanation for the observed floor on damped Lyman alpha (DLA) systems metallicities reported in the literature, which is of this order. We find that stellar metallicities do not necessarily trace stellar ages, as mergers of halos with established stellar populations can create superpositions of t-Z evolutionary tracks. A bimodal metallicity distribution is created after a starburst occurs when the halo can cool efficiently through atomic line cooling.Comment: 11 pages, 7 figures; replaced with accepted version to ApJ; additional movies and images can be found at http://www.astro.princeton.edu/~jwise/research/GalaxyBirth.htm

Neurocognitive therapeutics: from concept to application in the treatment of negative attention bias

There is growing interest in the use of neuroimaging for the direct treatment of mental illness. Here, we present a new framework for such treatment, neurocognitive therapeutics. What distinguishes neurocognitive therapeutics from prior approaches is the use of precise brain-decoding techniques within a real-time feedback system, in order to adapt treatment online and tailor feedback to individuals’ needs. We report an initial feasibility study that uses this framework to alter negative attention bias in a small number of patients experiencing significant mood symptoms. The results are consistent with the promise of neurocognitive therapeutics to improve mood symptoms and alter brain networks mediating attentional control. Future work should focus on optimizing the approach, validating its effectiveness, and expanding the scope of targeted disorders