scholarly journals Reduced chemical scheme for modelling warm to hot hydrogen-dominated atmospheres

2019 ◽  
Vol 624 ◽  
pp. A58 ◽  
Author(s):  
O. Venot ◽  
R. Bounaceur ◽  
M. Dobrijevic ◽  
E. Hébrard ◽  
T. Cavalié ◽  
...  

Context. Three-dimensional models that account for chemistry are useful tools to predict the chemical composition of (exo)planet and brown dwarf atmospheres and interpret observations of future telescopes, such as James Webb Space Telescope (JWST) and Atmospheric Remote-sensing Infrared Exoplanet Large-survey (ARIEL). Recent Juno observations of the NH3 tropospheric distribution in Jupiter also indicate that 3D chemical modelling may be necessary to constrain the deep composition of the giant planets of the solar system. However, due to the high computational cost of chemistry calculations, 3D chemical modelling has so far been limited. Aims. Our goal is to develop a reduced chemical scheme from the full chemical scheme of Venot et al. 2012 (A&A, 546, A43) able to reproduce accurately the vertical profiles of the observable species (H2O, CH4, CO, CO2, NH3, and HCN). This reduced scheme should have a size compatible with three-dimensional models and be usable across a large parameter space (e.g. temperature, pressure, elemental abundance). The absence of C2H2 from our reduced chemical scheme prevents its use to study hot C-rich atmospheres. Methods. We used a mechanism-processing utility program designed for use with Chemkin-Pro to reduce a full detailed mechanism. The ANSYS© Chemkin-Pro Reaction Workbench allows the reduction of a reaction mechanism for a given list of target species and a specified level of accuracy. We took a warm giant exoplanet with solar abundances, GJ 436b, as a template to perform the scheme reduction. To assess the validity of our reduced scheme, we took the uncertainties on the reaction rates into account in Monte Carlo runs with the full scheme, and compared the resulting vertical profiles with the reduced scheme. We explored the range of validity of the reduced scheme even further by applying our new reduced scheme to GJ 436b’s atmosphere with different elemental abundances, to three other exoplanet atmospheres (GJ 1214b, HD 209458b, HD 189733b), a brown dwarf atmosphere (SD 1110), and to the troposphere of two giant planets of the solar system (Uranus and Neptune). Results. For all cases except one, the abundances predicted by the reduced scheme remain within the error bars of the model with the full scheme. Expectedly, we found important differences that cannot be neglected only for the C-rich hot atmosphere. The reduced chemical scheme allows more rapid runs than the full scheme from which it is derived (~30× faster). Conclusions. We have developed a reduced scheme containing 30 species and 181 reversible reactions. This scheme has a large range of validity and can be used to study all kinds of warm atmospheres, except hot C-rich ones that contain a high amount of C2H2. It can be used in 1D models, for fast computations, but also in 3D models for hot giant (exo)planet and brown dwarf atmospheres.

1975 ◽  
Vol 39 (8) ◽  
pp. 544-546
Author(s):  
HL Wakkerman ◽  
GS The ◽  
AJ Spanauf

2020 ◽  
Vol 17 (4) ◽  
pp. 342-351
Author(s):  
Sergio A. Durán-Pérez ◽  
José G. Rendón-Maldonado ◽  
Lucio de Jesús Hernandez-Diaz ◽  
Annete I. Apodaca-Medina ◽  
Maribel Jiménez-Edeza ◽  
...  

Background: The protozoan Giardia duodenalis, which causes giardiasis, is an intestinal parasite that commonly affects humans, mainly pre-school children. Although there are asymptomatic cases, the main clinical features are chronic and acute diarrhea, nausea, abdominal pain, and malabsorption syndrome. Little is currently known about the virulence of the parasite, but some cases of chronic gastrointestinal alterations post-infection have been reported even when the infection was asymptomatic, suggesting that the cathepsin L proteases of the parasite may be involved in the damage at the level of the gastrointestinal mucosa. Objective: The aim of this study was the in silico identification and characterization of extracellular cathepsin L proteases in the proteome of G. duodenalis. Methods: The NP_001903 sequence of cathepsin L protease from Homo sapienswas searched against the Giardia duodenalisproteome. The subcellular localization of Giardia duodenaliscathepsin L proteases was performed in the DeepLoc-1.0 server. The construction of a phylogenetic tree of the extracellular proteins was carried out using the Molecular Evolutionary Genetics Analysis software (MEGA X). The Robetta server was used for the construction of the three-dimensional models. The search for possible inhibitors of the extracellular cathepsin L proteases of Giardia duodenaliswas performed by entering the three-dimensional structures in the FINDSITEcomb drug discovery tool. Results: Based on the amino acid sequence of cathepsin L from Homo sapiens, 8 protein sequences were identified that have in their modular structure the Pept_C1A domain characteristic of cathepsins and two of these proteins (XP_001704423 and XP_001704424) are located extracellularly. Threedimensional models were designed for both extracellular proteins and several inhibitory ligands with a score greater than 0.9 were identified. In vitrostudies are required to corroborate if these two extracellular proteins play a role in the virulence of Giardia duodenalisand to discover ligands that may be useful as therapeutic targets that interfere in the mechanism of pathogenesis generated by the parasite. Conclusion: In silicoanalysis identified two proteins in the Giardia duodenalisprotein repertoire whose characteristics allowed them to be classified as cathepsin L proteases, which may be secreted into the extracellular medium to act as virulence factors. Three-dimensional models of both proteins allowed the identification of inhibitory ligands with a high score. The results suggest that administration of those compounds might be used to block the endopeptidase activity of the extracellular cathepsin L proteases, interfering with the mechanisms of pathogenesis of the protozoan parasite Giardia duodenalis.


2011 ◽  
Vol 49 (4) ◽  
pp. 326-327 ◽  
Author(s):  
Karen A. Eley ◽  
Robin Richards ◽  
Dermot Dobson ◽  
Alf Linney ◽  
Stephen R. Watt-Smith

Sign in / Sign up

Export Citation Format

Share Document