A multiphysics and multiscale software environment for modeling astrophysical systems

We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a “Noah’s Ark” milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.     

Radio imaging of the Subaru/XMM–Newton Deep Field – II. The 37 brightest radio sources

We study the 37 brightest radio sources in the Subaru/ XMM–Newton Deep Field. We have spectroscopic redshifts for 24 of 37 objects and photometric redshifts for the remainder, yielding a median redshift z _med for the whole sample of   z _med≃ 1.1  and a median radio luminosity close to the 'Fanaroff–Riley type I/type II (FR I/FR II)' luminosity divide. Using mid-infrared (mid-IR) ( Spitzer MIPS 24 μm) data we expect to trace nuclear accretion activity, even if it is obscured at optical wavelengths, unless the obscuring column is extreme. Our results suggest that above the FR I/FR II radio luminosity break most of the radio sources are associated with objects that have excess mid-IR emission, only some of which are broad-line objects, although there is one clear low-accretion-rate object with an FR I radio structure. For extended steep-spectrum radio sources, the fraction of objects with mid-IR excess drops dramatically below the FR I/FR II luminosity break, although there exists at least one high-accretion-rate 'radio-quiet' QSO. We have therefore shown that the strong link between radio luminosity (or radio structure) and accretion properties, well known at z ∼ 0.1, persists to z ∼ 1. Investigation of mid-IR and blue excesses shows that they are correlated as predicted by a model in which, when significant accretion exists, a torus of dust absorbs ∼30 per cent of the light, and the dust above and below the torus scatters ≳1 per cent of the light.     

The orientation of sorted stripes in the maritime subantarctic,Marion Island

The orientation of sorted stripes developed in glacial deposits on Marion Island is examined. This study confirms earlier reports of preferential occurrence of sorted stripes on windward slopes. However, sorted stripes were also found to occur on low angle leeward slopes. Mechanisms for the orientation of sorted stripes by wind action are discussed. Copyright © 2001 John Wiley & Sons, Ltd.     

Deep-sea reef fish assemblage patterns on the Blake Plateau(Western North Atlantic Ocean)

Deep‐water coral habitats are scattered throughout slope depths (360–800 m) off the Southeastern United States (SEUS, Cape Lookout, North Carolina, to Cape Canaveral, Florida), contributing substantial structure and diversity to bottom habitats. In some areas (e.g. off North Carolina) deep corals form nearly monotypic (Lophelia pertusa) high profile mounds, and in other areas (e.g. off Florida) many species may colonize hard substrata. Deep coral and hard substrata ecosystems off the SEUS support a unique fish assemblage. Using the Johnson‐Sea‐Link submersible (in 2000–2005, 65 dives), and a remotely operated vehicle (in 2003, five dives), fishes were surveyed in nine deep reef study areas along the SEUS slope. Forty‐two benthic reef fish species occurred in deep reef habitats in these study areas. Species richness was greatest on the two coral banks off Cape Lookout, North Carolina (n = 23 and 27 species) and lowest on the two sites off Cape Canaveral, Florida (n = 7 and 8 species). Fish assemblages exhibited significantly (ANOSIM, Global R = 0.69, P = 0.001) different patterns among sites. Stations sampled off North Carolina (three study areas) formed a distinct group that differed from all dives conducted to the south. Although several species defined the fish assemblages at the North Carolina sites, Laemonema barbatulum, Laemonema melanurum, and Helicolenus dactylopterus generally had the most influence on the definition of the North Carolina group. Fish assemblages at three sites within the central survey area on the Blake Plateau were also similar to each other, and were dominated by Nezumia sclerorhynchus and L. melanurum. Synaphobranchus spp. and Neaumia sclerorhynchus differentiated the two southern sites off Cape Canaveral, Florida, from the other station groups. Combinations of depth and habitat type had the most influence on these station groups; however, explicit mechanisms contributing to the organization of these assemblages remain unclear.     

Factors affecting spatial and temporal variability in material exchange between the Southern Everglades wetlands and Florida Bay (USA)

Physical and biological processes controlling spatial and temporal variations in material concentration and exchange between the Southern Everglades wetlands and Florida Bay were studied for 2.5 years in three of the five major creek systems draining the watershed. Daily total nitrogen (TN), and total phosphorus (TP) fluxes were measured for 2 years in Taylor River, and ten 10-day intensive studies were conducted in this creek to estimate the seasonal flux of dissolved inorganic nitrogen (N), phosphorus (P), total organic carbon (TOC), and suspended matter. Four 10-day studies were conducted simultaneously in Taylor, McCormick, and Trout Creeks to study the spatial variation in concentration and flux. The annual fluxes of TOC, TN, and TP from the Southern Everglades were estimated from regression equations. The Southern Everglades watershed, a 460-km² area that includes Taylor Slough and the area south of the C-111 canal, exported 7.1 g C m⁻², 0.46 g N m⁻², and 0.007 g P m⁻², annually. Everglades P flux is three to four orders of magnitude lower than published flux estimates from wetlands influenced by terrigenous sedimentary inputs. These low P flux values reflect both the inherently low P content of Everglades surface water and the efficiency of Everglades carbonate sediments and biota in conserving and recycling this limiting nutrient. The seasonal variation of freshwater input to the watershed was responsible for major temporal variations in N, P, and C export to Florida Bay; approximately 99% of the export occurred during the rainy season. Wind-driven forcing was most important during the later stages of the dry season when low freshwater head coincided with southerly winds, resulting in a net import of water and materials into the wetlands. We also observed an east to west decrease in TN:TP ratio from 212:1 to 127:1. Major spatial gradients in N:P ratios and nutrient concentration and flux among the creek were consistent with the westward decrease in surface water runoff from the P-limited Everglades and increased advection of relatively P-rich Gulf of Mexico (GOM) waters into Florida Bay. Comparison of measured nutrient flux from Everglades surface water inputs from this study with published estimates of other sources of nutrients to Florida Bay (i.e. atmospheric deposition, anthropogenic inputs from the Florida Keys, advection from the GOM) show that Everglades runoff represents only 2% of N inputs and 0.5% of P input to Florida Bay.     

A Paddock to reef monitoring and modelling framework for the Great Barrier Reef: Paddock and catchment component

Targets for improvements in water quality entering the Great Barrier Reef (GBR) have been set through the Reef Water Quality Protection Plan (Reef Plan). To measure and report on progress towards the targets set a program has been established that combines monitoring and modelling at paddock through to catchment and reef scales; the Paddock to Reef Integrated Monitoring, Modelling and Reporting Program (Paddock to Reef Program). This program aims to provide evidence of links between land management activities, water quality and reef health. Five lines of evidence are used: the effectiveness of management practices to improve water quality; the prevalence of management practice adoption and change in catchment indicators; long-term monitoring of catchment water quality; paddock & catchment modelling to provide a relative assessment of progress towards meeting targets; and finally marine monitoring of GBR water quality and reef ecosystem health. This paper outlines the first four lines of evidence.     

A note on climate change adaptation for seaports: a challenge for global ports, a challenge for global society

With 80 % of world trade carried by sea, seaports provide crucial linkages in global supply-chains and are essential for the ability of all countries to access global markets. Seaports are likely to be affected directly and indirectly by climatic changes, with broader implications for international trade and development. Due to their coastal location, seaports are particularly vulnerable to extreme weather events associated with increasing sea levels and tropical storm activity, as illustrated by hurricane “Sandy”. In view of their strategic role as part of the globalized trading system, adapting ports in different parts of the world to the impacts of climate change is of considerable importance. Reflecting the views of a diverse group of stakeholders with expertise in climate science, engineering, economics, policy, and port management, this essay highlights the climate change challenge for ports and suggests a way forward through the adoption of some initial measures. These include both “soft” and “hard” adaptations that may be spearheaded by individual port entities, but will require collaboration and support from a broad range of public and private sector stakeholders and from society at large. In particular, the essay highlights a need to shift to more holistic planning, investment and operation.     

A realistic model for point-sources imaged on array detectors: The model and initial results

We have constructed a computer model for simulation of point-sources imaged on two-dimensional detectors. An attempt has been made to ensure that the model produces data that mimic real data taken with 2-D detectors. To be realistic, such simulations must include randomly generated noise of the appropriate type from all sources (e.g. source, background, and detector). The model is generic and accepts input values for parameters such as pixel size, read noise, source magnitude, and sky brightness. Point-source profiles are then generated with noise and detector characteristics added via our model. The synthetic data are output as simple integrations (onedimensional), as radial slices (two-dimensional), and as intensity-contour plots (three-dimensional). Each noise source can be turned on or off so that they can be studied separately as well as in combination to yield a realistic view of an image. This paper presents the basic properties of the model and some examples of how it can be used to simulate the effects of changing image position, image scale, signal strength, noise characteristics, and data reduction procedures.Use of the model has allowed us to confirm and quantify three points: 1) The use of traditionalsize apertures for photometry of faint point-sources adds substantial noise to the measurement which can significantly degrade the quality of the observation; 2) The number of pixels used to estimate the background is important and must be considered when estimating errors; and 3) The CCD equation normally used by the astronomical community consistently overestimates the signal-to-noise obtainable by a measurement while a revised equation, discussed here, provides a better estimator.     

Reconstructing epilimnetic total phosphorus using diatoms: statistical and ecological constraints

Diatoms respond rapidly to eutrophication and diatom-based models for inferring total phosphorus (TP) have found wide application in palaeolimnology, especially in tracking trajectories of past and recent nutrient enrichment and in establishing pre-disturbance targets for restoration. Using new analysis of existing training sets and sediment-cores we examine the statistical and ecological constraints of diatom-inferred TP (DI-TP) models. Although the models show an apparently strong relationship between measured and inferred TP in the training sets, even under cross-validation, the models display three fundamental weaknesses, namely (1) the relationship between TP and diatom relative abundance is heavily confounded with secondary variables such as alkalinity and lake depth, (2) the models contain many taxa that are not significantly related to TP, and (3) comparison between different models shows poor or no spatial replicability. At some sites the sediment-core diatom assemblage change tracks the TP gradient in the training sets and DI-TP reconstructions are consistent with monitored TP data and known catchment histories for the recent past. At others diatom species turnover is apparently related to variables other than TP, and DI-TP fails to even reproduce plausible trends. Pre-disturbance DI-TP values are also questionable at most sites. We argue that these problems pervade many DI-TP models, particularly those where violations of the basic assumptions of the transfer function approach are ignored.