| 1. |
- Shameer, S., et al.
(author)
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TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
- 2015
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 43:D1, s. D637-D644
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Journal article (peer-reviewed)abstract
- The metabolic network of a cell represents thecatabolic and anabolic reactions that interconvertsmall molecules (metabolites) through the activity ofenzymes, transporters and non-catalyzed chemicalreactions. Our understanding of individual metabolicnetworks is increasing as we learn more aboutthe enzymes that are active in particular cells underparticular conditions and as technologies advanceto allow detailed measurements of the cellularmetabolome. Metabolic network databases areof increasing importance in allowing us to contextualisedata sets emerging from transcriptomic,proteomic and metabolomic experiments. Here wepresent a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describesthe generic and condition-specific metabolic networkof Trypanosoma brucei, a parasitic protozoan responsiblefor human and animal African trypanosomiasis.In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have alsoimplemented a network-based representation of theinformation through MetExplore, yielding a novel environmentin which to visualise the metabolism ofthis important parasite.
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| 2. |
- Maaskant, K. M., et al.
(author)
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Location and sizes of forsterite grains in protoplanetary disks Interpretation from the Herschel DIGIT programme
- 2015
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 574
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Journal article (peer-reviewed)abstract
- Context. The spectra of protoplanetary disks contain mid-and far-infrared emission features produced by forsterite dust grains. The spectral features contain information about the forsterite temperature, chemical composition and grain size. Aims. We aim to characterize how the 23 and 69 pm features can be used to constrain the physical locations of forsterite in disks. We check for consistency between two independent forsterite temperature measurements: the I-23/I-69 feature strength ratio and the shape of the 69 pm band. Methods. We performed radiative transfer modeling to study the effect of disk properties to the forsterite spectral features. Temperature-dependent forsterite opacities were considered in self-consistent models to compute forsterite emission from protoplanetary disks. Results. Modelling grids are presented to study the effects of grain size, disk gaps, radial mixing and optical depth to the forsterite features. Independent temperature estimates derived from the I-23/I-69 feature strength ratio and the 69 pm band shape are most inconsistent for HD 141569 and Oph IRS 48. A case study of the disk of HD 141569 shows two solutions to fit the forsterite spectrum. A model with T similar to 40 K, iron-rich (similar to 0-1% Fe) and 1 pm forsterite grains, and a model with warmer (T similar to 100 K), iron-free, and larger (10 pm) grains. Conclusions. We find that for disks with low upper limits of the 69 pm feature (most notably in flat, self-shadowed disks), the forsterite must be hot, and thus close to the star. We find no correlation between disk gaps and the presence or absence of forsterite features. We argue that the 69 pm feature of the evolved transitional disks HD 141569 and Oph IRS 48 is most likely a tracer of larger (i.e. >= 10 mu m) forsterite grains.
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| 3. |
- Chen, Tao, et al.
(author)
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Formation of H2 from internally heated polycyclic aromatic hydrocarbons : Excitation energy dependence
- 2015
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 142:14
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Journal article (peer-reviewed)abstract
- We have investigated the effectiveness of molecular hydrogen (H-2) formation from Polycyclic Aromatic Hydrocarbons (PAHs) which are internally heated by collisions with keV ions. The present and earlier experimental results are analyzed in view of molecular structure calculations and a simple collision model. We estimate that H-2 formation becomes important for internal PAH temperatures exceeding about 2200 K, regardless of the PAH size and the excitation agent. This suggests that keV ions may effectively induce such reactions, while they are unlikely due to, e.g., absorption of single photons with energies below the Lyman limit. The present analysis also suggests that H-2 emission is correlated with multi-fragmentation processes, which means that the [PAH-2H](+) peak intensities in the mass spectra may not be used for estimating H-2-formation rates.
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| 4. |
- Chen, Tao, et al.
(author)
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From planes to bowls : Photodissociation of the bisanthenequinone cation
- 2018
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In: Chemical Physics Letters. - : Elsevier B.V.. - 0009-2614 .- 1873-4448. ; 692, s. 298-303
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Journal article (peer-reviewed)abstract
- We present a combined experimental and theoretical study of the photodissociation of the bisanthenequinone (C28H12O2) cation, Bq+. The experiments show that, upon photolysis, the Bq+ cation does not dehydrogenate, but instead fragments through the sequential loss of the two neutral carbonyl groups, causing the formation of five-membered carbon cycles. Quantum chemical calculations confirm this Bq+ → [Bq - CO]+ → [Bq - 2CO]+ sequence as the energetically most favorable reaction pathway. For the first CO loss, a transition state with a barrier of ∼3.2 eV is found, substantially lower than the lowest calculated H loss dissociation pathway (∼4.9 eV). A similar situation applies for the second CO loss channel (∼3.8 eV vs. ∼4.7 eV), but where the first dissociation step does not strongly alter the planar PAH geometry, the second step transforms the molecule into a bowl-shaped one.
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| 5. |
- Chen, Tao, et al.
(author)
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Photodissociation processes of Bisanthenquinone cation
- 2017
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In: Proceedings of the International Astronomical Union. - : Cambridge University Press. - 1743-9213. ; :S332, s. 353-359
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Journal article (peer-reviewed)abstract
- A systematic study, using ion trap time-of-flight mass spectrometry, is presented for the photo-dissociation processes of Bisanthenquinone (Bq) cations, C28H12O2+, a ketone substituted Polycyclic Aromatic Hydrocarbon (PAH). The Bq cation fragments through sequential loss of the two neutral carbonyl (CO) units upon laser (626nm) irradiation, resulting in a PAH-like derivative C26H12+. Upon further irradiation, C26H12+ exhibits both stepwise dehydrogenation and C2/C2H2 loss fragmentation channels. Quantum chemistry calculations reveal a detailed picture for the first CO-loss, which involves a transition state with a barrier of ∼ 3.4 eV, which is lower than the energy required for the lowest H-loss pathway (∼ 5.0 eV). The barrier for the second CO-loss is higher (∼ 4.9 eV). The subsequent loss of this unit changes the Bq geometry from a planar to a bent one. It is concluded that the photodissociation mechanism of the substituted PAH cations studied here is site selective in the substituted subunit. This work also shows that an acetone substituted PAH cation is not photo-stable upon irradiation.
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| 6. |
- Cordiner, M. A., et al.
(author)
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On the Nature of the Enigmatic Object IRAS 19312+1950: A Rare Phase of Massive Star Formation?
- 2016
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In: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 828:1
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Journal article (peer-reviewed)abstract
- IRAS 19312+1950 is a peculiar object that has eluded firm characterization since its discovery, with combined maser properties similar to an evolved star and a young stellar object (YSO). To help determine its true nature, we obtained infrared spectra of IRAS 19312+1950 in the range 5–550 μm using the Herschel and Spitzer space observatories. The Herschel PACS maps exhibit a compact, slightly asymmetric continuum source at 170 μm, indicative of a large, dusty circumstellar envelope. The far-IR CO emission line spectrum reveals two gas temperature components: ≈0.22 solar masses of material at 280 ± 18 K, and ≈1.6 solar masses of material at 157 ± 3 K. The O i 63 μm line is detected on-source but no significant emission from atomic ions was found. The HIFI observations display shocked, high-velocity gas with outflow speeds up to 90 km/s along the line of sight. From Spitzer spectroscopy, we identify ice absorption bands due to H2O at 5.8 μm and CO2 at 15 μm. The spectral energy distribution is consistent with a massive, luminous (~2 × 10^4 solar luminosities) central source surrounded by a dense, warm circumstellar disk and envelope of total mass ~500–700 solar masses, with large bipolar outflow cavities. The combination of distinctive far-IR spectral features suggest that IRAS 19312+1950 should be classified as an accreting, high-mass YSO rather than an evolved star. In light of this reclassification, IRAS 19312+1950 becomes only the fifth high-mass protostar known to exhibit SiO maser activity, and demonstrates that 18 cm OH maser line ratios may not be reliable observational discriminators between evolved stars and YSOs.
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