An Unsplit Godunov Method for Ideal MHD via Constrained Transport

We describe a single step, second-order accurate Godunov scheme for ideal MHD based on combining the piecewise parabolic method (PPM) for performing spatial reconstruction, the corner transport upwind (CTU) method of Colella for multidimensional integration, and the constrained transport (CT) algorithm for preserving the divergence-free constraint on the magnetic field. We adopt the most compact form of CT, which requires the field be represented by area-averages at cell faces. We demonstrate that the fluxes of the area-averaged field used by CT can be made consistent with the fluxes of the volume-averaged field returned by a Riemann solver if they obey certain simple relationships. We use these relationships to derive new algorithms for constructing the CT fluxes at grid cell corners which reduce exactly to the equivalent one-dimensional solver for plane-parallel, grid-aligned flow. We show that the PPM reconstruction algorithm must include multidimensional terms for MHD, and we describe a number of important extensions that must be made to CTU in order for it to be used for MHD with CT. We present the results of a variety of test problems to demonstrate the method is accurate and robust.Comment: 45 pages, 13 figures, accepted for publication in J. Comp. Phys., More information on Athena can be found at http://www.astro.princeton.edu/~jstone/athena.htm

High-radiation-zone design of the FMIT high-energy beam transport

The Fusion Materials Irradiation Test (FMIT) deuteron linac, operating at 35 MeV and 100 mA continuous duty, is expected to spill 3 ..mu..A/m and to lose 10 ..mu..A at specific bending-magnet positions. The major impact of this spill will be felt in the High-Energy Beam Transport (HEBT), where many beam-line components must be maintained. A modular design concept, that uses segmented termination panels remotely located from the modules, is being employed. Radiation-hardened quadrupoles can be opened, clamshell fashion, to release the water-cooled beam tube replacement if there is beam damage or lithium contamination from the target. Termination panels contain electrical, water, and instrumentation fittings to service the module, and are positioned to allow room for neutron-absorbing shielding between the beamline and the panel. The modular construction allows laboratory prealignment and check-out of all components on a structural carriage and is adaptable to supporting gamma shields

Formal Alliances, 1816-1965: an Extension of the Basic Data

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69121/2/10.1177_002234336900600305.pd

Unraveling Twisty Linear Polarization Morphologies in Black Hole Images

We investigate general relativistic magnetohydrodynamic simulations (GRMHD) to determine the physical origin of the twisty patterns of linear polarization seen in spatially resolved black hole images and explain their morphological dependence on black hole spin. By characterising the observed emission with a simple analytic ring model, we find that the twisty morphology is determined by the magnetic field structure in the emitting region. Moreover, the dependence of this twisty pattern on spin can be attributed to changes in the magnetic field geometry that occur due to the frame dragging. By studying an analytic ring model, we find that the roles of Doppler boosting and lensing are subdominant. Faraday rotation may cause a systematic shift in the linear polarization pattern, but we find that its impact is subdominant for models with strong magnetic fields and modest ion-to-electron temperature ratios. Models with weaker magnetic fields are much more strongly affected by Faraday rotation and have more complicated emission geometries than can be captured by a ring model. However, these models are currently disfavoured by the recent EHT observations of M87*. Our results suggest that linear polarization maps can provide a probe of the underlying magnetic field structure around a black hole, which may then be usable to indirectly infer black hole spins. The generality of these results should be tested with alternative codes, initial conditions, and plasma physics prescriptions.Comment: 25 pages, 19 figure

A new measurement of the Collins and Sivers asymmetries on a transversely polarised deuteron target

New high precision measurements of the Collins and Sivers asymmetries of charged hadrons produced in deep-inelastic scattering of muons on a transversely polarised 6LiD target are presented. The data were taken in 2003 and 2004 with the COMPASS spectrometer using the muon beam of the CERN SPS at 160 GeV/c. Both the Collins and Sivers asymmetries turn out to be compatible with zero, within the present statistical errors, which are more than a factor of 2 smaller than those of the published COMPASS results from the 2002 data. The final results from the 2002, 2003 and 2004 runs are compared with naive expectations and with existing model calculations.Comment: 40 pages, 28 figure

An Empirical Strategy for Characterizing Bacterial Proteomes across Species in the Absence of Genomic Sequences

Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300–500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide synthesis and cofactor biosynthesis, allowing classification of bacteria by observation of conserved processes. Additionally, within these core functionalities, we observed proteins involved in the alternative lactate utilization pathway, recently described in Shewanella

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.Peer reviewe