We have developed pLink, software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link identification and is compatible with multiple homo- or hetero-bifunctional cross-linkers. We validated the program with proteins of known structures, and we further tested it on protein complexes, crude immunoprecipitates and whole-cell lysates. We show that it is a robust tool for protein-structure and protein-protein-interaction studies.

For the Antennae interacting galaxy pair, we have obtained high quality, fully sampled 12 CO J=1-0 and 3-2 maps of the regions surrounding the nuclei and the area of overlap between the two galaxies. The maps possess an angular resolution of 15 ′′ or 1.5 kpc, so far the highest resolution maps available at both the J=1-0 and 3-2 transitions. In addition, 12 CO J=2-1 data have been obtained for the positions of the two nuclei as well as in part of the overlap region with 20 ′′ angular resolution. The 12 CO J=1-0, 2-1, 3-2 emission all peak in an off-nucleus region adjacent to where the two disks overlap. Use of the conventional X factor yields ∼ 4 × 10 9 M ⊙ molecular gas mass in the overlap region. It is difficult to understand how such a large amount of molecular gas can be accumulated in this region given the relatively short lifetime of molecular clouds and the limited period of time for this region to form.Line emission at 13 CO J=2-1 and 3-2 is detected at selected points in the two nuclei and the overlap region. Both the 12 CO/ 13 CO J=2-1 and 3-2 integrated intensity ratios are remarkably high in the overlap region. This is the first published case in which such high 12 CO/ 13 CO J=2-1 and 3-2 ratios are found outside a galactic nucleus. Detailed LVG modeling indicates that the 12 CO and 13 CO emission originate in different spatial components. The 12 CO emission may originate within a non-virialized low density gas component with a large velocity gradient. Assuming a CO-to-H 2 abundance ratio of 10 −4 , the X factor given by the LVG model is an order of magnitude lower than the conventional value for molecular clouds in the Milky Way, but it scales inversely as the assumed value for this ratio. Accordingly, we suggest the possibility that the strong CO emission in the overlap region of the Antennae galaxies is associated with increased radiative efficiency, possibly caused by a large velocity dispersion within the individual molecular clouds.A comparison of the CO J=3-2 emission with the SCUBA 850 µm continuum in the Antennae galaxies shows that the CO line emission contributes globally 46% of the 850 µm continuum flux and that the ratio of 12 CO J=3-2 to SCUBA 850 µm flux varies by a factor of two across the system. After correcting for the 12 CO J=3-2 contamination, the dust emission at 850 µm detected by SCUBA is consistent with the thermal emission from a single warm dust component with a mass of 1.7 ×10 7 M ⊙ .

In this paper we present the first observations of the Ophiuchus molecular cloud performed as part of the James Clerk Maxwell Telescope (JCMT) Gould Belt Survey (GBS) with the SCUBA-2 instrument. We demonstrate methods for combining these data with previous HARP CO, Herschel, and IRAM N 2 H + observations in order to accurately quantify the properties of the SCUBA-2 sources in Ophiuchus. We produce a catalogue of all of the sources found by SCUBA-2. We separate these into protostars and starless cores. We list all of the starless cores and perform a full virial analysis, including external pressure. This is the first time that external pressure has been included in this level of detail. We find that the majority of our cores are either bound or virialised. Gravitational energy and external pressure are on average of a similar order of magnitude, but with some variation from region to region. We find that cores in the Oph A region are gravitationally bound prestellar cores, while cores in the Oph C and E regions are pressure-confined. We determine that N 2 H + is a good tracer of the bound material of prestellar cores, although we find some evidence for N 2 H + freezeout at the very highest core densities. We find that non-thermal linewidths decrease substantially between the gas traced by C 18 O and that traced by N 2 H + , indicating the dissipation of turbulence at higher densities. We find that the critical Bonnor-Ebert stability criterion is not a good indicator of the boundedness of our cores. We detect the pre-brown dwarf candidate Oph B-11 and find a flux density and mass consistent with previous work. We discuss regional variations in the nature of the cores and find further support for our previous hypothesis of a global evolutionary gradient across the cloud from southwest to northeast, indicating sequential star formation across the region.

We present the 13 CO/C 18 O (J = 3 → 2) Heterodyne Inner Milky Way Plane Survey (CHIMPS) which has been carried out using the Heterodyne Array Receiver Program on the 15 m James Clerk Maxwell Telescope (JCMT) in Hawaii. The high-resolution spectral survey currently covers |b| ≤ 0. • 5 and 28 • l 46 • , with an angular resolution of 15 arcsec in 0.5 km s −1 velocity channels. The spectra have a median rms of ∼ 0.6 K at this resolution, and for optically thin gas at an excitation temperature of 10 K, this sensitivity corresponds to column densities of N H 2 ∼ 3 × 10 20 cm −2 and N H 2 ∼ 4 × 10 21 cm −2 for 13 CO and C 18 O, respectively. The molecular gas that CHIMPS traces is at higher column densities and is also more optically thin than in other publicly available CO surveys due to its rarer isotopologues, and thus more representative of the three-dimensional structure of the clouds. The critical density of the J = 3 → 2 transition of CO is 10 4 cm −3 at temperatures of ≤ 20 K, and so the higher density gas associated with star formation is well traced. These data complement other existing Galactic plane surveys, especially the JCMT Galactic Plane Survey which has similar spatial resolution and column density sensitivity, and the Herschel infrared Galactic Plane Survey. In this paper, we discuss the observations, data reduction and characteristics of the survey, presenting integrated emission maps for the region covered. Position velocity diagrams allow comparison with Galactic structure models of the Milky Way, and while we find good agreement with a particular four arm model, there are some significant deviations.

Abstract. The Taffy Galaxies system, UGC 12914/5, contains huge amounts of molecular gas in the bridge region between the receding spirals after a direct collision. 2−9 × 10 9 M of molecular gas is present between the galaxies, more than the CO emission from the entire Milky Way! Such dense gas can only be torn off by collisions between dense clouds, in this case with relative velocities of about 800 km s −1 , such that the remnant cloud acquires an intermediate velocity and is left in the bridge after separation of the colliding galaxies. We suggest that after ionization in the collision front, the gas cooled and recombined very quickly such that the density remained high and the gas left the colliding disks in molecular form.

We present a comprehensive study of the dust and gas properties in the after-head-on-collision UGC 12914/15 galaxy system using multitransition CO data and SCUBA submillimeter continuum images at both 450 and 850 m. CO(3Y2) line emission was detected in the disks of UGC 12914 and UGC 12915, as well as in a bridge connecting the two galaxies. Dust emission at 450 m was detected for the first time in the two galactic disks and in the connecting bridge. Using a large velocity gradient excitation analysis model we have obtained good estimates of the physical parameters in different regions of this system, and the amount of molecular gas was found to be 3Y 4 times lower than that estimated by other investigators using the standard Galactic CO-to-H 2 conversion factor. Comparing with the dust mass derived from the SCUBA data, we found that the gas-to-dust ratio was comparable to the Galactic value in the two galaxy disks but a factor of $3 higher in the bridge. The physical condition of the molecular gas in the bridge is comparable to that in the diffuse clouds in our Galaxy. Our result is consistent with the scenario that the bridge molecular gas originated from the disk molecular clouds and has been drawn out of the galactic disks due to direct cloud-cloud collision. Our data indicate that the global star formation efficiency (SFE; L IR /M H 2 ) in UGC 12915 is comparable to that of normal spiral galaxies, and the SFE is 40% lower in UGC 12914 than in UGC 12915. Little star formation activity was found in the bridge except in an H ii region adjacent to the disk of UGC 12915.

We present large-area maps of the CO J=3-2 emission obtained at the James Clerk Maxwell Telescope for four spiral galaxies in the Virgo Cluster. We combine these data with published CO J=1-0, 24 µm, and Hα images to measure the CO line ratios, molecular gas masses, and instantaneous gas depletion times. For three galaxies in our sample (NGC 4254, NGC4321, and NGC 4569), we obtain molecular gas masses of 7 × 10 8 − 3 × 10 9 M ⊙ and disk-averaged instantaneous gas depletion times of 1.1-1.7 Gyr. We argue that the CO J=3-2 line is a better tracer of the dense star forming molecular gas than the CO J=1-0 line, as it shows a better correlation with the star formation rate surface density both within and between galaxies. NGC 4254 appears to have a larger star formation efficiency(smaller gas depletion time), perhaps because it is on its first passage through the Virgo Cluster. NGC 4569 shows a large-scale gradient in the gas properties traced by the CO J=3-2/J=1-0 line ratio, which suggests that its interaction with the intracluster medium is affecting the dense star-forming portion of the interstellar medium directly. The fourth galaxy in our sample, NGC 4579, has weak CO J=3-2 emission despite having bright 24 µm emission; however, much of the central luminosity in this galaxy may be due to the presence of a central AGN.

We present BIMA two-field mosaic CO(1-0) images of the Taffy galaxies (UGC 12914/15), which show the distinct taffy-like radio continuum emission bridging the two spiral disks. Large amounts of molecular gas (1.4 x 10^{10} Msun, using the standard Galactic CO-to-H$_2$ conversion applicable to Galactic disk giant molecular clouds [GMCs]) were clearly detected throughout the taffy bridge between the two galaxies, which, as in the more extreme case of HI, presumably results from a head-on collision between the two galaxies. The highest CO concentration between the two galaxies corresponds to the H_alpha source in the taffy bridge near the intruder galaxy UGC 12915. This HII region is also associated with the strongest source of radio continuum in the bridge, and shows both morphological and kinematic connections to UGC 12915. The overall CO distribution of the entire system agrees well with that of the radio continuum emission, particularly in the taffy bridge. This argues for the star formation origin of a significant portion of the radio continuum emission. Compared to the HI morphology and kinematics, which are strongly distorted owing to the high-speed collision, CO better defines the orbital geometry and impact parameter of the interaction, as well as the disk properties (e.g., rotation, orientation) of the progenitor galaxies. Based on the 20cm-to-CO ratio maps, we conclude that the starburst sites are primarily located in UGC 12915 and the H_alpha source in the bridge and show that the molecular gas in the taffy bridge is forming into stars with star formation efficiency comparable to that of the target galaxy UGC 12914 and similar to that in the Galactic disk.Comment: Minor typo/style corrections to match with the published version (AJ, Nov. issue). A single .ps.gz file of the entire paper can be downloaded from http://spider.ipac.caltech.edu/staff/gao/Taffy/all.ps.g