The Vertical Structure of Planet-induced Gaps in Proto-Planetary Discs

Giant planets embedded in circumstellar discs are expected to open gaps in these discs. We examine the vertical structure of the gap edges. We find that the planet excites spiral arms with significant (Mach number of a half) vertical motion of the gas, and discuss the implications of these motions. In particular, the spiral arms will induce strong vertical stirring of the dust, making the edge appeared `puffed up' relative to the bulk of the disc. Infra-red observations (sensitive to dust) would be dominated by the light from the thick inner edge of the disc. Sub-millimetre observations (sensitive to gas velocities) would appear to be hot in `turbulent' motions (actually the ordered motion caused by the passage of the spiral arms), but cold in chemistry. Resolved sub-millimetre maps of circumstellar discs might even be able to detect the spiral arms directly.Comment: Revision adds new data, and corrects physical intepretatio

A survey of volatile species in Oort cloud comets C/2001 Q4 (NEAT) and C/2002 T7 (LINEAR) at millimeter wavelengths

The line emission in the coma was measured in the comets C/2001 Q4 (NEAT) and C/2002 T7 (LINEAR), that were observed on five consecutive nights, 7-11 May 2004, at heliocentric distances of 1.0 and 0.7 AU, respectively, by means of high-resolution spectroscopy using the 10-m Submillimeter Telescope (SMT). We present a search for six parent- and product-volatile species (HCN, H2CO, CO, CS, CH3OH, and HNC) in both comets. Multiline observations of the CH3OH J = 5-4 series allow us to estimate the rotational temperature using the rotation diagram technique. We derive rotational temperatures of 54(9) K for C/2001 Q4 (NEAT) and 119(34) K for C/2002 T7 (LINEAR) that are roughly consistent with observations of other comets at similar distances from the Sun. The gas production rates of material are computed using a spherically symmetric molecular excitation code that includes collisions between neutrals and electrons. We find an HCN production rate of 2.96(5)e26 molec.s-1 for comet C/2001 Q4 (NEAT), corresponding to a mixing ratio with respect to H2O of 1.12(2)e-3. The mean HCN production rate during the observing period is 4.54(10)e26 molec.s-1 for comet C/2002 T7 (LINEAR), which gives a Q_HCN/Q_H2O mixing ratio of 1.51(3)e-3. With systematically lower mixing ratios in comet C/2001 Q4 (NEAT), production rate ratios of the observed species with respect to H2O lie within the typical ranges of dynamically new comets in both objects. We find a relative low abundance of CO in C/2001 Q4 (NEAT) compared to the observed range in other comets based on millimeter/submillimeter observations, and a significant upper limit on the CO production in C/2002 T7 (LINEAR) is derived. Depletion of CO suggests partial evaporation from the surface layers during previous visits to the outer Solar System and agrees with previous measurements of dynamically new comets.Comment: 20 pages, 18 figures. Minor changes to match the published versio

Computational biology tools in design of an agrochemical against Xyllela fastidiosa.

Xylella fastidiosa is a Gram-negative, non-flagellated bacterium that causes CVC in citrus and Pierce?s disease in grapevines. The CVC affects 40% of the 200 million orange trees in São Paulo state. It colonizes the xylem vessels of the plants, blocking the water and nutrient flows. PilT protein is a part of the motility system and very important for Xyllela pathogenicity and our protein target for drug design. Computational biology tools were used to design the compound able to inhibit the formation of the PilT hexamer, leading to loss of Xyllela pathogenicity. This approach could be employed in the development of new inhibitors against different targets belonging to the same protein family of PilT

Computational Biology tools in design of an agrochemical against Xylella fastidiosa.

Since its pathogenicity is related to bacterial motility, the protein PilT from the twitching motility system has been chosen as the host target. Using rational drug design, based on a detailed comprehension of the protein host structure, small molecules were designed in order to block the activity of the protein and provoke the loss of the bacterium pathogenicity.C.016

Advanced 3D “Modeling” and “Printing” for the Surgical Planning of a Successful Case of Thoraco-Omphalopagus Conjoined Twins Separation

The surgical separation of two Conjoined Twins is a particularly complex operation. Surgical times are particularly long and post-operative complications are very frequent in this type of procedure. We report a clinical case of surgical separation of two thoraco-omphalopagus conjoined twins in which, thanks to the use of (3D) three dimensional technologies, we were able to significantly reduce operative times and improve clinical outcomes

Measuring molecular abundances in comet C/2014 Q2 (Lovejoy) using the APEX telescope

Comet composition provides critical information on the chemical and physical processes that took place during the formation of the Solar system. We report here on millimetre spectroscopic observations of the long-period bright comet C/2014 Q2 (Lovejoy) using the Atacama Pathfinder Experiment (APEX) band 1 receiver between 2015 January UT 16.948 to 18.120, when the comet was at heliocentric distance of 1.30 AU and geocentric distance of 0.53 AU. Bright comets allow for sensitive observations of gaseous volatiles that sublimate in their coma. These observations allowed us to detect HCN, CH3OH (multiple transitions), H2CO and CO, and to measure precise molecular production rates. Additionally, sensitive upper limits were derived on the complex molecules acetaldehyde (CH3CHO) and formamide (NH2CHO) based on the average of the strongest lines in the targeted spectral range to improve the signal-to-noise ratio. Gas production rates are derived using a non-LTE molecular excitation calculation involving collisions with H2O and radiative pumping that becomes important in the outer coma due to solar radiation. We find a depletion of CO in C/2014 Q2 (Lovejoy) with a production rate relative to water of 2 per cent, and relatively low abundances of Q(HCN)/Q(H2O), 0.1 per cent, and Q(H2CO)/Q(H2O), 0.2 per cent. In contrast the CH3OH relative abundance Q(CH3OH)/Q(H2O), 2.2 per cent, is close to the mean value observed in other comets. The measured production rates are consistent with values derived for this object from other facilities at similar wavelengths taking into account the difference in the fields of view. Based on the observed mixing ratios of organic molecules in four bright comets including C/2014 Q2, we find some support for atom addition reactions on cold dust being the origin of some of the molecules.Comment: 10 pages, 7 figures, to be published in MNRA

Submillimetric spectroscopic observations of volatiles in comet C/2004 Q2 (Machholz)

We aim to determine the production rates of several parent and product volatiles and the 12C/13C isotopic carbon ratio in the long-period comet C/2004 Q2 (Machholz), which is likely to originate from the Oort Cloud. The line emission from several molecules in the coma was measured with high signal-to-noise ratio in January 2005 at heliocentric distance of 1.2 AU by means of high-resolution spectroscopic observations using the Submillimeter Telescope (SMT). We have obtained production rates of several volatiles (CH3OH, HCN, H13CN, HNC, H2CO, CO and CS) by comparing the observed and simulated line-integrated intensities. Furthermore, multiline observations of the CH3OH (7-6) series allow us to estimate the rotational temperature using the rotation diagram technique. We find that the CH3OH population distribution of the levels sampled by these lines can be described by a rotational temperature of 40 \pm 3 K. Derived mixing ratios relative to hydrogen cyanide are CO/CH3OH/H2CO/CS/HNC/H13CN/HCN = 30.9/24.6/4.8/0.57/0.031/0.013/1 assuming a pointing offset of 8" due to the uncertain ephemeris at the time of the observations and the telescope pointing error. The measured relative molecular abundances in C/2004 Q2 (Machholz) are between low- to typical values of those obtained in Oort Cloud comets, suggesting that it has visited the inner solar system previously and undergone thermal processing. The HNC/HCN abundance ratio of ~3.1% is comparable to that found in other comets, accounting for the dependence on the heliocentric distance, and could possibly be explained by ion-molecule chemical processes in the low-temperature atmosphere. From a tentative H13CN detection, the measured value of 97 \pm 30 for the H12CN/H13CN isotopologue pair is consistent with a telluric value.Comment: 14 pages with 11 figures, abridged abstrac

Electrostatic potential at the alpha carbon atoms along the alpha helices and beta strands.

We present here analysis of pre-calculated values for the electrostatic potential at the alpha carbons, previously stored in the STING_RDB.PABMB

Signature contact coordination patterns for secondary structure elements in protein structures.

We present here analysis of pre-calculated values for the cross-links, previously stored in the STING_RDB.PABMB

Studying structure function relationship of proteins using "remediated" PDB files.

We have invested a significant amount of time and CPU resources in order to curate and analyze what ate the consequences for in-silico analysis of the active site 3D environment after implementing remediated PDB files to STING_DB and STING interface.PABMB