Perpendicular-current Studies of Electron Transport Across Metal/Metal Interfaces

We review what we have learned about the scattering of electrons by the interfaces between two different metals (M1/M2) in the current-perpendicular-to-plane (CPP) geometry. In this geometry, the intrinsic quantity is the specific resistance, AR, the product of the area through which the CPP current flows times the CPP resistance. We describe results for both non-magnetic/non-magnetic (N1/N2) and ferromagnetic/non-magnetic (F/N) pairs. We focus especially upon cases where M1/M2 are lattice matched (i.e., have the same crystal structure and the same lattice parameters to within ~ 1%), because in these cases no-free-parameter calculations of 2AR agree surprisingly well with measured values. But we also list and briefly discuss cases where M1/M2 are not lattice matched, either having different crystal structures, or lattice parameters that differ by several percent. The published calculations of 2AR in these latter cases do not agree so well with measured values.Comment: 6 pages, 2 figures, 2 tables. In Press: Applied Surface Scienc

Merging clusters of galaxies observed with XMM-Newton

We present results from the XMM-Newton observations of our ongoing program on merging clusters. To date three clusters have been observed, covering the temporal sequence from early to late stage mergers: A1750, A2065 and A3921. Using spatially-resolved spectroscopy of discrete regions, hardness ratio and temperature maps, we show that all three clusters display a complex temperature structure. In the case of A1750, a double cluster, we argue that the observed temperature structure is not only related to the ongoing merger but also to previous merger events. A2065 seems an excellent example of a `compact merger', i.e. when the centres of the two clusters have just started to interact, producing a shock in the ICM. Using comparisons with numerical simulations and complementary optical data, the highly complex temperature structure evident in A3921 is interpreted as an off-axis merger between two unequal mass components. These results illustrate the complex physics of merger events. The relaxation time can be larger than the typical time between merger events, so that the present day morphology of clusters depends not only on on-going interaction but also on the more ancient formation history.Comment: 10 pages, 3 figures. Use elsart.cls. Accepted for publication in Advances in Space Research. A version with full resolution figures can be found at http://www.star.bris.ac.uk/elena/cospar_3clusters.pd

Self Consistent Molecular Field Theory for Packing in Classical Liquids

Building on a quasi-chemical formulation of solution theory, this paper proposes a self consistent molecular field theory for packing problems in classical liquids, and tests the theoretical predictions for the excess chemical potential of the hard sphere fluid. Results are given for the self consistent molecular fields obtained, and for the probabilities of occupancy of a molecular observation volume. For this system, the excess chemical potential predicted is as accurate as the most accurate prior theories, particularly the scaled particle (Percus-Yevick compressibility) theory. It is argued that the present approach is particularly simple, and should provide a basis for a molecular-scale description of more complex solutions.Comment: 6 pages and 5 figure

Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites [preprint]

The human genome contains roughly 1,600 transcription factors (TFs) (1), DNA-binding proteins recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX (2), and in vivo, using techniques including ChIP-seq (3, 4). We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog derived from thousands of ENCODE Phase II and III ChIP-seq experiments and HT-SELEX experiments; this motif catalog is integrated with the ENCODE registry of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites. The database also offers novel tools for applying the motif models within machine learning frameworks and using these models for integrative analysis, including annotation of variants and disease and trait heritability. We will continue to expand the resource as ENCODE Phase IV data are released

Substructure of the galaxy clusters in the REXCESS sample: observed statistics and comparison to numerical simulations

We study the substructure statistics of a representative sample of galaxy clusters by means of two currently popular substructure characterisation methods, power ratios and centroid shifts. We use the 31 clusters from the REXCESS sample, compiled from the southern ROSAT All-Sky cluster survey REFLEX with a morphologically unbiased selection in X-ray luminosity and redshift, all of which have been reobserved with XMM-Newton. We investigate the uncertainties of the substructure parameters and examine the dependence of the results on projection effects, finding that the uncertainties of the parameters can be quite substantial. Thus while the quantification of the dynamical state of individual clusters with these parameters should be treated with extreme caution, these substructure measures provide powerful statistical tools to characterise trends of properties in large cluster samples. The centre shift parameter, w, is found to be more sensitive in general. For the REXCESS sample neither the occurence of substructure nor the presence of cool cores depends on cluster mass. There is a significant anti-correlation between the existence of substantial substructure and cool cores. The simulated clusters show on average larger substructure parameters than the observed clusters, a trend that is traced to the fact that cool regions are more pronounced in the simulated clusters, leading to stronger substructure measures in merging clusters and clusters with offset cores. Moreover, the frequency of cool regions is higher in the simulations than in the observations, implying that the description of the physical processes shaping cluster formation in the simulations requires further improvement.Comment: Mauscript submitted to Astronomy and Astrophysics, 20 figure

The Representative XMM-Newton Cluster Structure Survey (REXCESS) of an X-ray Luminosity Selected Galaxy Cluster Sample

The largest uncertainty for cosmological studies using clusters of galaxies is introduced by our limited knowledge of the statistics of galaxy cluster structure, and of the scaling relations between observables and cluster mass. To improve on this situation we have started an XMM-Newton Large Programme for the in-depth study of a representative sample of 33 galaxy clusters, selected in the redshift range z=0.055 to 0.183 from the REFLEX Cluster Survey, having X-ray luminosities above 0.4 X 10^44 h_70^-2 erg s^-1 in the 0.1 - 2.4 keV band. This paper introduces the sample, compiles properties of the clusters, and provides detailed information on the sample selection function. We describe the selection of a nearby galaxy cluster sample that makes optimal use of the XMM-Newton field-of-view, and provides nearly homogeneous X-ray luminosity coverage for the full range from poor clusters to the most massive objects in the Universe. For the clusters in the sample, X-ray fluxes are derived and compared to the previously obtained fluxes from the ROSAT All-Sky Survey. We find that the fluxes and the flux errors have been reliably determined in the ROSAT All-Sky Survey analysis used for the REFLEX Survey. We use the sample selection function documented in detail in this paper to determine the X-ray luminosity function, and compare it with the luminosity function of the entire REFLEX sample. We also discuss morphological peculiarities of some of the sample members. The sample and some of the background data given in this introductory paper will be important for the application of these data in the detailed studies of cluster structure, to appear in forthcoming publications.Comment: 17 pages, 17 figures; to appear in A&A. A pdf version with full-quality figures can be found at ftp://ftp.xray.mpe.mpg.de/people/gwp/xmmlp/xmmlp.pd

Exploring the galaxy cluster-group transition regime at high redshifts: Physical properties of two newly detected z > 1 systems

Context: Multi-wavelength surveys for clusters of galaxies are opening a window on the elusive high-redshift (z>1) cluster population. Well controlled statistical samples of distant clusters will enable us to answer questions about their cosmological context, early assembly phases and the thermodynamical evolution of the intracluster medium. Aims: We report on the detection of two z>1 systems, XMMU J0302.2-0001 and XMMU J1532.2-0836, as part of the XMM-Newton Distant Cluster Project (XDCP) sample. We investigate the nature of the sources, measure their spectroscopic redshift and determine their basic physical parameters. Methods: The results of the present paper are based on the analysis of XMM-Newton archival data, optical/near-infrared imaging and deep optical follow-up spectroscopy of the clusters. Results: We confirm the X-ray source XMMU J0302.2-0001 as a gravitationally bound, bona fide cluster of galaxies at spectroscopic redshift z=1.185. We estimate its M500 mass to (1.6+/-0.3) times 10^{14} Msun from its measured X-ray luminosity. This ranks the cluster among intermediate mass system. In the case of XMMU J1532.2-0836 we find the X-ray detection to be coincident with a dynamically bound system of galaxies at z=1.358. Optical spectroscopy reveals the presence of a central active galactic nucleus, which can be a dominant source of the detected X-ray emission from this system. We provide upper limits of X-ray parameters for the system and discuss cluster identification challenges in the high-redshift low-mass cluster regime. A third, intermediate redshift (z=0.647) cluster, XMMU J0302.1-0000, is serendipitously detected in the same field as XMMU J0302.2-0001. We provide its analysis as well.Comment: Accepted to A&A, 13/04/2011. 15 pages, 18 figures, 5 tables, 2 appendice

The large-scale shock in the cluster of galaxies Hydra A

We analyzed a deep XMM-Newton observation of the cluster of galaxies Hydra A, focusing on the large-scale shock discovered as a surface brightness discontinuity in Chandra images. The shock front can be seen both in the pressure map and in temperature profiles in several sectors. The Mach numbers determined from the temperature jumps are in good agreement with the Mach numbers derived from EPIC/pn surface brightness profiles and previously from Chandra data and are consistent with M~1.3. The estimated shock age in the different sectors using a spherically symmetric point explosion model ranges between 130 and 230 Myr and the outburst energy between 1.5 and 3e61 ergs. The shape of the shock seen in the pressure map can be approximated with an ellipse centered 70 kpc towards the NE from the cluster center. We aimed to develop a better model that can explain the offset between the shock center and the AGN and give a consistent result on the shock age and energy. To this end, we performed 3D hydrodynamical simulations in which the shock is produced by a symmetrical pair of AGN jets launched in a spherical galaxy cluster. As an explanation of the observed offset of the shock center, we consider large-scale bulk flows in the intracluster medium. The simulation successfully reproduces the size, ellipticity, and average Mach number of the observed shock front. The predicted age of the shock is 160 Myr and the total input energy 3e61 erg. Both values are within the range determined by the spherically symmetric model. Matching the observed 70 kpc offset of the shock ellipse from the cluster center requires large-scale coherent motions with a high velocity of 670 km/s. We discuss the feasibility of this scenario and offer alternative ways to produce the offset and to further improve the simulation.Comment: 14 pages, accepted for publication in A&A, minor revision compared to previous versio

Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers

Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall curve (PR-AUC) of DNase peaks by 17.5-166.7% and that of H3K27ac peaks by 7.1-22.2%. We further improved this differential signal method using multiple contrast tissues. Evaluated using a blind test, the differential H3K27ac signal method substantially improved PR-AUC from 0.48 to 0.75 for predicting heart enhancers. We further validated our approach using postnatal retina and cerebral cortex enhancers identified by massively parallel reporter assays, and observed improvements for both tissues. In summary, we compared nine peak callers and devised a superior method for predicting tissue-specific mouse developmental enhancers by reranking the called peaks

LoCuSS: Comparison of Observed X-ray and Lensing Galaxy Cluster Scaling Relations with Simulations

The Local Cluster Substructure Survey (LoCuSS, Smith et al.) is a systematic multi-wavelength survey of >100 X-ray luminous galaxy clusters (0.14<z<0.3) selected from the ROSAT all sky survey. We used data on 37 LoCuSS clusters from the XMM-Newton archive to investigate the global scaling relations of galaxy clusters. The scaling relations based solely on the X-ray data obey empirical self-similarity and reveal no additional evolution beyond the LSS growth. Weak lensing mass measurements are also available in the literature for 19 of the clusters with XMM-Newton data. The average of the weak lensing mass to X-ray based mass ratio is 1.09+/-8, setting the limit of the non-thermal pressure support to 9+/-8%. The mean of the weak lensing mass to X-ray based mass ratio of these clusters is ~1 with 31-51% scatter. The scatter in the mass--observable relations (M-Y_X, M-M_{gas} and M-T) is smaller using X-ray based masses than using weak lensing masses by a factor of 2. Using the scaled radius defined by the Y_X profile, we obtain lower scatter in the weak lensing mass based mass--observable relations. The normalization of the M-Y_X relation (also M-M_{gas} and M-T relations) using X-ray (weak lensing) mass estimates is lower than the one from simulations by up to 20% at ~3 sigma (~2 sigma) significance. Despite the large scatter in the X-ray to lensing comparison, the agreement between these two completely independent observational methods is an important step towards controlling astrophysical and measurement systematics in cosmological scaling relations.Comment: 56 pages, 32 figure, 2008A&A...482..451Z, typos corrected in Table A.