MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map

Advances in electron microscopy (EM) allow for structure determination of large biological assemblies at increasingly higher resolutions. A key step in this process is fitting multiple component structures into an EM-derived density map of their assembly. Here, we describe a web server for this task. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The output is an ensemble of models ranked by their quality of fit to the density map. The models can be viewed online or downloaded from the website. The service is available at; http://salilab.org/multifit/ and http://bioinfo3d.cs.tau.ac.il/

The Vela Pulsar in the Near-Infrared

We report on the first detection of the Vela pulsar in the near-infrared with the VLT/ISAAC in the Js and H bands. The pulsar magnitudes are Js=22.71 +/- 0.10 and H=22.04 +/- 0.16. We compare our results with the available multiwavelength data and show that the dereddened phase-averaged optical spectrum of the pulsar can be fitted with a power law F_nu propto nu^(-alpha_nu) with alpha_nu = 0.12 +/- 0.05, assuming the color excess E(B-V)=0.055 +/-0.005 based on recent spectral fits of the emission of the Vela pulsar and its supernova remnant in X-rays. The negative slope of the pulsar spectrum is different from the positive slope observed over a wide optical range in the young Crab pulsar spectrum. The near-infrared part of the Vela spectrum appears to have the same slope as the phase-averaged spectrum in the high energy X-ray tail, obtained in the 2-10 keV range with the RXTE. Both of these spectra can be fitted with a single power law suggesting their common origin. Because the phase-averaged RXTE spectrum in this range is dominated by the second X-ray peak of the pulsar light curve, coinciding with the second main peak of its optical pulse profile, we suggest that this optical peak can be redder than the first one. We also detect two faint extended structures in the 1.5''-3.1'' vicinity of the pulsar, projected on and aligned with the south-east jet and the inner arc of the pulsar wind nebula, detected in X-rays with Chandra. We discuss their possible association with the nebula.Comment: 12 pages, 8 figures, accepted for publication in A&A, the associated near-infrared images in the fits format are available at http://www.ioffe.ru/astro/NSG/obs/vela-ir

The identification of the optical companion to the binary millisecond pulsar J0610-2100 in the Galactic field

We have used deep V and R images acquired at the ESO Very Large Telescope to identify the optical companion to the binary pulsar PSR J0610-2100, one of the black-widow millisecond pulsars recently detected by the Fermi Gamma-ray Telescope in the Galactic plane. We found a faint star (V~26.7) nearly coincident (\delta r ~0".28) with the pulsar nominal position. This star is visible only in half of the available images, while it disappears in the deepest ones (those acquired under the best seeing conditions), thus indicating that it is variable. Although our observations do not sample the entire orbital period (P=0.28 d) of the pulsar, we found that the optical modulation of the variable star nicely correlates with the pulsar orbital period and describes a well defined peak (R~25.6) at \Phi=0.75, suggesting a modulation due to the pulsar heating. We tentatively conclude that the companion to PSR J0610-2100 is a heavily ablated very low mass star (~ 0.02Msun) that completely filled its Roche Lobe.Comment: 17 pages, 5 figures - Accepted for pubblication in Ap

HST/WFPC2 observations of the LMC pulsar PSR B0540-69

The study of the younger, and brighter, pulsars is important to understand the optical emission properties of isolated neutron stars. PSRB0540-69, the second brightest (V~22) optical pulsar, is obviously a very interesting target for these investigations. The aim of this work is threefold: constraining the pulsar proper motion and its velocity on the plane of the sky through optical astrometry, obtaining a more precise characterisation of the pulsar optical spectral energy distribution (SED) through a consistent set of multi-band, high-resolution, imaging photometry observations, measuring the pulsar optical phase-averaged linear polarisation, for which only a preliminary and uncertain measurement was obtained so far from ground-based observations. We performed high-resolution observations of PSRB0540-69 with the WFPC2 aboard the HST, in both direct imaging and polarimetry modes. From multi-epoch astrometry we set a 3sigma upper limit of 1 mas/yr on the pulsar proper motion, implying a transverse velocity <250 km/s at the 50 kpc LMC distance. Moreover, we determined the pulsar absolute position with an unprecedented accuracy of 70 mas. From multi-band photometry we characterised the pulsar power-law spectrum and we derived the most accurate measurement of the spectral index (0.70+/-0.07) which indicates a spectral turnover between the optical and X-ray bands. Finally, from polarimetry we obtained a new measurement of the pulsar phase-averaged polarisation degree (16+/-4%),consistent with magnetosphere models depending on the actual intrinsic polarisation degree and depolarisation factor, and we found that the polarisation vector (22+/-12deg position angle) is possibly aligned with the semi-major axis of the pulsar-wind nebula and with the apparent proper motion direction of its bright emission knot.Comment: 14 pages, 12 figures, accepted for publication in Astronomy & Astrophysic

The 3D Structure of N132D in the LMC: A Late-Stage Young Supernova Remnant

We have used the Wide Field Spectrograph (WiFeS) on the 2.3m telescope at Siding Spring Observatory to map the [O III] 5007{\AA} dynamics of the young oxygen-rich supernova remnant N132D in the Large Magellanic Cloud. From the resultant data cube, we have been able to reconstruct the full 3D structure of the system of [O III] filaments. The majority of the ejecta form a ring of ~12pc in diameter inclined at an angle of 25 degrees to the line of sight. We conclude that SNR N132D is approaching the end of the reverse shock phase before entering the fully thermalized Sedov phase of evolution. We speculate that the ring of oxygen-rich material comes from ejecta in the equatorial plane of a bipolar explosion, and that the overall shape of the SNR is strongly influenced by the pre-supernova mass loss from the progenitor star. We find tantalizing evidence of a polar jet associated with a very fast oxygen-rich knot, and clear evidence that the central star has interacted with one or more dense clouds in the surrounding ISM.Comment: Accepted for Publication in Astrophysics & Space Science, 18pp, 8 figure

Pictor A (PKS 0518-45) - From Nucleus to Lobes

We present radio and optical imaging and kinematic data for the radio galaxy Pictor A, including HST continuum and [OIII], emission-line images (at a resolution of 25 - 100 mas) and ground-based imaging and spectroscopy (at a resolution of ~ 1.5". The radio data include 3 cm Australia Telescope images of the core, at a resolution comparable to that of the optical, ground-based images, and a VLBI image of a jet in the compact core (at a resolution of 2 - 25 mas), which seems to align with a continuum ``jet'' found in the HST images. The core radio jet, the HST optical continuum ``jet'', and the NW H-alpha filaments all appear to point toward the optical-synchrotron hot-spot in the NW lobe of this object and are associated with a disrupted velocity field in the extended ionized gas. The ground-based spectra which cover this trajectory also yield line ratios for the ionized gas which have anomalously low [NII] (6564), suggesting either a complex, clumpy structure in the gas with a higher cloud-covering factor at larger radii and with denser clouds than is found in the nuclear regions of most NLRG and Seyfert 2 galaxies, or some other, unmodeled, mechanism for the emergent spectrum from this region. The H-alpha emission-line filaments to the N appear to be associated with a 3 cm radio continuum knot which lies in a gap in the filaments ~ 4" from the nucleus. Altogether, the data in this paper provide good circumstantial evidence for non-disruptive redirection of a radio jet by interstellar gas clouds in the host galaxy.Comment: 19 pages, 6 ps.gz fig pages, to appear in the Ap.J. Supp

The near-infrared detection of PSR B0540-69 and its nebula

The ~1700 year old PSR B0540-69 in the LMC is considered the twin of the Crab pulsar because of its similar spin parameters, magnetic field, and energetics. Its optical spectrum is fit by a power-law, ascribed to synchrotron radiation, like for the young Crab and Vela pulsars. nIR observations, never performed for PSR B0540-69, are crucial to determine whether the optical power-law spectrum extends to longer wavelengths or a new break occurs, like it happens for both the Crab and Vela pulsars in the mIR, hinting at an even more complex particle energy and density distribution in the pulsar magnetosphere. We observed PSR B0540-69 in the J, H, and Ks bands with the VLT to detect it, for the first time, in the nIR and characterise its optical-to-nIR spectrum. To disentangle the pulsar emission from that of its pulsar wind nebula (PWN), we obtained high-spatial resolution adaptive optics images with NACO. We could clearly identify PSR B0540-69 in our J, H, and Ks-band images and measure its flux (J=20.14, H=19.33, Ks=18.55, with an overall error of +/- 0.1 magnitudes in each band). The joint fit to the available optical and nIR photometry with a power-law spectrum gives a spectral index alpha=0.70 +/-0.04. The comparison between our NACO images and HST optical ones does not reveal any apparent difference in the PWN morphology as a function of wavelength. The PWN optical-to-nIR spectrum is also fit by a single power-law, with spectral index alpha=0.56+/- 0.03, slightly flatter than the pulsar's. Using NACO at the VLT, we obtained the first detection of PSR B0540-69 and its PWN in the nIR. Due to the small angular scale of the PWN (~4") only the spatial resolution of the JWST will make it possible to extend the study of the pulsar and PWN spectrum towards the mid-IR.Comment: 11 pages, 10 figures, Accepted for publication on Astronomy and Astrophysic

The Biological Standard of Living in the two Germanies.

Physical stature is used as a proxy for the biological standard of living in the two Germanies before and after unification in an analysis of a cross-sectional sample (1998) of adult heights, as well as among military recruits of the 1990s. West Germans tended to be taller than East Germans throughout the period under consideration. Contrary to official proclamations of a classless society, there were substantial social differences in physical stature in East-Germany. Social differences in height were greater in the East among females, and less among males than in the West. The difficulties experienced by the East-German population after 1961 is evident in the increase in social inequality of physical stature thereafter, as well as in the increasing gap relative to the height of the West-German population. After unification, however, there is a tendency for East-German males, but not of females, to catch up with their West-German counterparts

Constraining the optical emission from the double pulsar system J0737-3039

We present the first optical observations of the unique system J0737-3039 (composed of two pulsars, hereafter PSR-A and PSR-B). Ultra-deep optical observations, performed with the High Resolution Camera of the Advanced Camera for Surveys on board the Hubble Space Telescope could not detect any optical emission from the system down to m_F435W=27.0 and m_F606W=28.3. The estimated optical flux limits are used to constrain the three-component (two thermal and one non-thermal) model recently proposed to reproduce the XMM-Newton X-ray spectrum. They suggest the presence of a break at low energies in the non-thermal power law component of PSR-A and are compatible with the expected black-body emission from the PSR-B surface. The corresponding efficiency of the optical emission from PSR-A's magnetosphere would be comparable to that of other Myr-old pulsars, thus suggesting that this parameter may not dramatically evolve over a time-scale of a few Myr.Comment: 16 pages, 3 figures, ApJ accepte

An extension of the SHARC survey

We report on our search for distant clusters of galaxies based on optical and X-ray follow up observations of X-ray candidates from the SHARC survey. Based on the assumption that the absence of bright optical or radio counterparts to possibly extended X-ray sources could be distant clusters. We have obtained deep optical images and redshifts for several of these objects and analyzed archive XMM-Newton or Chandra data where applicable. In our list of candidate clusters, two are probably galaxy structures at redshifts of z$\sim$0.51 and 0.28. Seven other structures are possibly galaxy clusters between z$\sim$0.3 and 1. Three sources are identified with QSOs and are thus likely to be X-ray point sources, and six more also probably fall in this category. One X-ray source is spurious or variable. For 17 other sources, the data are too sparse at this time to put forward any hypothesis on their nature. We also serendipitously detected a cluster at z=0.53 and another galaxy concentration which is probably a structure with a redshift in the [0.15-0.6] range. We discuss these results within the context of future space missions to demonstrate the necessity of a wide field of view telescope optimized for the 0.5-2 keV range.Comment: Accepted in A&