Calculation of linelists for Chromium Hydride (CrH) & Manganese Hydride (MnH)

New linelists (list of wavelengths with associated frequencies) for the open-shell transition metal diatomics Chromium Hydride (CrH) and Manganese Hydride (MnH) have been calculated. These linelists have been calculated from first principles making use of the Born-Oppenheimer approximation which decomposes the Schr\"{o}dinger equation for a molecule into an electronic equation and rovibronic equation. To solve the electronic Schr\"{o}dinger equation and thus produce Potential Energy Curves (PECs), Dipole Moment Curves (DMCs) and all relevant couplings (transition dipole, electronic angular momentum, spin-orbit) the MRCI (Multi-Reference Configuration Interaction) method as implemented in the \textit{ab initio} \texttt{MOLPRO} package was used. The electronic states considered were those up to $20\;000$ cm$^{-1}$ as this region is of most importance to astronomers to whom we are creating the linelists for within the ExoMol project. The construction of linelists for transition metal diatomics is very much at a developmental stage due to the myriad of low-lying electronic states of high multiplicity which couple together. Hence during the calculation of \textit{ab initio} curves a systematic study of the CASSCF orbitals used for the proceeding MRCI calculations was undertaken for both CrH and MnH. Also the effect of changing the configuration space of electrons was found to have profound effects on the behaviour of the PECs obtained. Additionally, the variation in properties obtained by changing the number of states calculated within a single MRCI calculation was investigated. A choice selection of these \textit{ab initio} curves were then implemented into the in-house programme Duo to produce linelists for CrH and MnH. These linelists were refined using available experimental data. At present, the existing linelist available for CrH in literature has 2 electronic states. Our new linelist is composed from 8 low-lying electronic states of CrH. CrH is used to classify L type dwarfs under the widely accepted classification scheme of Kirkpatrick. Additionally it has been shown theoretically that CrH could be used as a sensitive probe of magnetic fields of stars and also in the so-called ``deuterium test'' to probe the evolutionary history of sub-stellar objects. Due to the limited coverage of the existing linelist, a new linelist is sought after by astronomers. At present MnH has not been discovered in outer space but due to the favourable abundance of manganese it has been speculated that it could be present in the ISM. Hence the creation of a linelist opens up the possibility of the first astronomical detection of this molecule. Since January 2016 I have been working as a teaching fellow at Aberystwyth University. Hence preliminary work has been done on creating projects for undergraduate students for the molecules of BeH, MgH and CaH. A summary of literature has also been created for FeH with a view to in future creating a new linelist for this molecule which is of considerable interest both from an astronomical and theoretical perspective

Bringing pupils into the ORBYTS of research

Most scientists would consider themselves lucky to publish a research paper while still an undergraduate, but a group of pupils at Highams Park School in East London has co-authored a paper at age 18, thanks to ORBYTS. Original Research By Young Twinkle Scientists (ORBYTS) comprises the core part of EduTwinkle, the education and outreach arm of the upcoming exoplanet space mission Twinkle, led by UK scientists and engineers, and is aimed at A-level students. ORBYTS was founded in 2016 by Clara Sousa-Silva, who was splitting her time teaching at Highams Park School and working as a postdoc at University College London, via the Researchers in Schools programme. This blend of education and research inspired her to set up a scheme enabling young postdoc and PhD students from her research group at UCL, ExoMol, to perform novel research with some of her sixth-form students. ORBYTS now involves more than 30 pupils in eight schools across the UK

ExoMol molecular line lists – XXVI: spectra of SH and NS

Line lists for the sulphur-containing molecules SH (the mercapto radical) and NS are computed as part of the ExoMol project. These line lists consider transitions within the X2Π ground state for 32SH, 33SH, 34SH,36SH and, 32SD, and 14N32S, 14N33S, 14N34S, 14N36S, and 15N32S. Ab initio potential energy (PEC) and spin-orbit coupling (SOC) curves are computed and then improved by fitting to experimentally observed transitions. Fully ab initio dipole moment curves (DMCs) computed at high level of theory are used to produce the final line lists. For SH, our fit gives a root-mean-square (rms) error of 0.03 cm−1 between the observed (⁠vmax = 4, Jmax = 34.5) and calculated transitions wavenumbers; this is extrapolated such that all X2Π rotational-vibrational-electronic (rovibronic) bound states are considered. For 32SH the resulting line list contains about 81 000 transitions and 2300 rovibronic states, considering levels up to vmax = 14 and Jmax = 60.5. For NS the refinement used a combination of experimentally determined frequencies and energy levels and led to an rms-fitting error of 0.002 cm−1. Each NS-calculated line list includes around 2.8 million transitions and 31 000 rovibronic states with a vibrational range up to v = 53 and rotational range up to J = 235.5, which covers up to 23 000 cm−1. Both line lists should be complete for temperatures up to 5000 K. Example spectra simulated using this line list are shown and comparisons made to the existing data in the CDMS data base. The line lists are available from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) data bases

Full Genome Characterization of the Culicoides-Borne Marsupial Orbiviruses: Wallal Virus, Mudjinbarry Virus and Warrego Viruses

Viruses belonging to the species Wallal virus and Warrego virus of the genus Orbivirus were identified as causative agents of blindness in marsupials in Australia during 1994/5. Recent comparisons of nucleotide (nt) and amino acid (aa) sequences have provided a basis for the grouping and classification of orbivirus isolates. However, full-genome sequence data are not available for representatives of all Orbivirus species. We report full-genome sequence data for three additional orbiviruses: Wallal virus (WALV); Mudjinabarry virus (MUDV) and Warrego virus (WARV). Comparisons of conserved polymerase (Pol), sub-core-shell 'T2' and core-surface 'T13' proteins show that these viruses group with other Culicoides borne orbiviruses, clustering with Eubenangee virus (EUBV), another orbivirus infecting marsupials. WARV shares <70% aa identity in all three conserved proteins (Pol, T2 and T13) with other orbiviruses, consistent with its classification within a distinct Orbivirus species. Although WALV and MUDV share <72.86%/67.93% aa/nt identity with other orbiviruses in Pol, T2 and T13, they share >99%/90% aa/nt identities with each other (consistent with membership of the same virus species - Wallal virus). However, WALV and MUDV share <68% aa identity in their larger outer capsid protein VP2(OC1), consistent with membership of different serotypes within the species - WALV-1 and WALV-2 respectively

ExoMol line lists - XLIV. IR and UV line list for silicon monoxide (SiO)

A new silicon monoxide (28Si16O) line list covering infrared, visible and ultraviolet regions called SiOUVenIR is presented. This line list extends the infrared EBJT ExoMol line list by including vibronic transitions to the A 1Π and E 1Σ+ electronic states. Strong perturbations to the A 1Π band system are accurately modelled through the treatment of 6 dark electronic states: C 1Σ−, D 1Δ, a 3Σ+, b 3Π, e 3Σ− and d 3Δ. Along with the X 1Σ+ ground state, these 9 electronic states were used to build a comprehensive spectroscopic model of SiO using a combination of empirical and ab initio curves, including the potential energy (PE), spin-orbit (SO), electronic angular momentum (EAM) and (transition) dipole moment curves. The ab initio PE and coupling curves, computed at the multireference configuration interaction (MRCI) level of theory, were refined by fitting their analytical representations to 2617 experimentally derived SiO energy levels determined from 97 vibronic bands belonging to the X–X, E–X and A–X electronic systems through the MARVEL procedure. 112 observed forbidden transitions from the C–X, D–X, e–X, and d–X bands were assigned using our predictions, and these could be fed back into the MARVEL procedure. The SiOUVenIR line list was computed using published ab initio transition dipole moments for the E–X and A–X bands; the line list is suitable for temperatures up to 10 000 K and for wavelengths longer than 140 nm. SiOUVenIR is available from www.exomol.com and the CDS database

ExoMol line lists - XLIV. IR and UV line list for silicon monoxide (SiO)

A new silicon monoxide (28Si16O) line list covering infrared, visible and ultraviolet regions called SiOUVenIR is presented. This line list extends the infrared EBJT ExoMol line list by including vibronic transitions to the A 1Π and E 1Σ+ electronic states. Strong perturbations to the A 1Π band system are accurately modelled through the treatment of 6 dark electronic states: C 1Σ−, D 1Δ, a 3Σ+, b 3Π, e 3Σ− and d 3Δ. Along with the X 1Σ+ ground state, these 9 electronic states were used to build a comprehensive spectroscopic model of SiO using a combination of empirical and ab initio curves, including the potential energy (PE), spin-orbit (SO), electronic angular momentum (EAM) and (transition) dipole moment curves. The ab initio PE and coupling curves, computed at the multireference configuration interaction (MRCI) level of theory, were refined by fitting their analytical representations to 2617 experimentally derived SiO energy levels determined from 97 vibronic bands belonging to the X–X, E–X and A–X electronic systems through the MARVEL procedure. 112 observed forbidden transitions from the C–X, D–X, e–X, and d–X bands were assigned using our predictions, and these could be fed back into the MARVEL procedure. The SiOUVenIR line list was computed using published ab initio transition dipole moments for the E–X and A–X bands; the line list is suitable for temperatures up to 10 000 K and for wavelengths longer than 140 nm. SiOUVenIR is available from www.exomol.com and the CDS database

The ExoMol database: Molecular line lists for exoplanet and other hot atmospheres

The ExoMol database (www.exomol.com) provides extensive line lists of molecular transitions which are valid over extended temperature ranges. The status of the current release of the database is reviewed and a new data structure is specified. This structure augments the provision of energy levels (and hence transition frequencies) and Einstein A coefficients with other key properties, including lifetimes of individual states, temperature-dependent cooling functions, Landé g-factors, partition functions, cross sections, k-coefficients and transition dipoles with phase relations. Particular attention is paid to the treatment of pressure broadening parameters. The new data structure includes a definition file which provides the necessary information for utilities accessing ExoMol through its application programming interface (API). Prospects for the inclusion of new species into the database are discussed

Cervical intramedullary schwannoma: a case report and review of the literature

Intramedullary schwannomas unrelated with neurofibromatosis are uncommon tumors, but if correctly diagnosed and properly treated they may have a good prognosis

AID-Targeting and Hypermutation of Non-Immunoglobulin Genes Does Not Correlate with Proximity to Immunoglobulin Genes in Germinal Center B Cells

Upon activation, B cells divide, form a germinal center, and express the activation induced deaminase (AID), an enzyme that triggers somatic hypermutation of the variable regions of immunoglobulin (Ig) loci. Recent evidence indicates that at least 25% of expressed genes in germinal center B cells are mutated or deaminated by AID. One of the most deaminated genes, c-Myc, frequently appears as a translocation partner with the Ig heavy chain gene (Igh) in mouse plasmacytomas and human Burkitt's lymphomas. This indicates that the two genes or their double-strand break ends come into close proximity at a biologically relevant frequency. However, the proximity of c-Myc and Igh has never been measured in germinal center B cells, where many such translocations are thought to occur. We hypothesized that in germinal center B cells, not only is c-Myc near Igh, but other mutating non-Ig genes are deaminated by AID because they are near Ig genes, the primary targets of AID. We tested this “collateral damage” model using 3D-fluorescence in situ hybridization (3D-FISH) to measure the distance from non-Ig genes to Ig genes in germinal center B cells. We also made mice transgenic for human MYC and measured expression and mutation of the transgenes. We found that there is no correlation between proximity to Ig genes and levels of AID targeting or gene mutation, and that c-Myc was not closer to Igh than were other non-Ig genes. In addition, the human MYC transgenes did not accumulate mutations and were not deaminated by AID. We conclude that proximity to Ig loci is unlikely to be a major determinant of AID targeting or mutation of non-Ig genes, and that the MYC transgenes are either missing important regulatory elements that allow mutation or are unable to mutate because their new nuclear position is not conducive to AID deamination