| 1. |
- Abelev, Betty, et al.
(författare)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 2. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 3. |
- Abelev, Betty, et al.
(författare)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
-
Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 4. |
- Binder, Manfred, et al.
(författare)
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Phylogenetic and phylogenomic overview of the Polyporales
- 2013
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Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 105:6, s. 1350-1373
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Tidskriftsartikel (refereegranskat)abstract
- We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000–49 900 00 bp and encode for 12 910–16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.
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| 5. |
- Curtis, Bruce A., et al.
(författare)
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 492:7427, s. 59-65
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Tidskriftsartikel (refereegranskat)abstract
- Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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| 6. |
- de Vries, Ronald P, et al.
(författare)
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Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
- 2017
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
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| 7. |
- Doubenskaia, Maria, et al.
(författare)
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Parametric analysis of SLM using comprehensive optical monitoring
- 2016
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Ingår i: Rapid prototyping journal. - : Emerald Group Publishing Limited. - 1355-2546 .- 1758-7670. ; 22:1, s. 40-50
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Tidskriftsartikel (refereegranskat)abstract
- Purpose - This paper aims to propose methods for on-line monitoring and process quality assurance of Selective Laser Melting (SLM) technology as a competitive advantage to enhance its implementation into modern manufacturing industry.Design/methodology/approach - Monitoring of thermal emission from the laser impact zone was carried out by an originally developed pyrometer and a charge-coupled device (CCD) camera which were integrated with the optical system of the PHENIX PM-100 machine. Experiments are performed with variation of the basic process parameters such as powder layer thickness (0-120 mu m), hatch distance (60-1,000 mu m) and fabrication strategy (the so-called "one-zone" and "two-zone").Findings - The pyrometer signal from the laser impact zone and the 2D temperature mapping from HAZ are rather sensible to variation of high-temperature phenomena during powder consolidation imposed by variation of the operational parameters.Research limitations/implications - Pyrometer measurements are in arbitrary units. This limitation is due to the difficulty to integrate diagnostic tools into the optical system of a commercial SLM machine.Practical implications - Enhancement of SLM process stability and efficiency through comprehensive optical diagnostics and on-line control.Originality/value - High-temperature phenomena in SLM were monitored coaxially with the laser beam for variation of several operational parameters.
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| 8. |
- Eshghi Sahraei, Shadi, et al.
(författare)
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Evolution and genomic signatures of arbuscular mycorrhizal fungi
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungi include at least two lineages of mutualistic plant symbionts, the arbuscular mycorrhizal fungi and the mycorrhizal fungi in Endogonales, as well as fungi with saprotrophic, pathogenic and endophytic life styles. Their evolutionary relationships remained enigmatic and the taxonomic rank is currently fluid. We recognize three phyla and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as the sister to Mucoromycota and Mortierellomycota. Analysis of gene family contractions and expansions indicate that arbuscular mycorrhizae (AM) fungi and Endogonales represent two independent transitions to mutualistic plant symbiosis and that these occurred early in the divergence of these lineages.
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| 9. |
- Floudas, Dimitrios, et al.
(författare)
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Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii
- 2015
-
Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 76, s. 78-92
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Tidskriftsartikel (refereegranskat)abstract
- Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited. (C) 2015 Elsevier Inc. All rights reserved.
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| 10. |
- Grigoriev, Igor A., et al.
(författare)
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A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation
- 2013
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Ingår i: Physics of fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 25:10, s. 105112-
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Tidskriftsartikel (refereegranskat)abstract
- The explicit algebraic Reynolds stress model of Wallin and Johansson [J. Fluid Mech. 403, 89 (2000)] is extended to compressible and variable-density turbulent flows. This is achieved by correctly taking into account the influence of the mean dilatation on the rapid pressure-strain correlation. The resulting model is formally identical to the original model in the limit of constant density. For two-dimensional mean flows the model is analyzed and the physical root of the resulting quartic equation is identified. Using a fixed-point analysis of homogeneously sheared and strained compressible flows, we show that the new model is realizable, unlike the previous model. Application of the model together with a K - omega model to quasi one-dimensional plane nozzle flow, transcending from subsonic to supersonic regime, also demonstrates realizability. Negative "dilatational" production of turbulence kinetic energy competes with positive "incompressible" production, eventually making the total production negative during the spatial evolution of the nozzle flow. Finally, an approach to include the baroclinic effect into the dissipation equation is proposed and an algebraic model for density-velocity correlations is outlined to estimate the corrections associated with density fluctuations. All in all, the new model can become a significant tool for CFD (computational fluid dynamics) of compressible flows.
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| 11. |
- Grigoriev, Igor A., et al.
(författare)
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Capturing turbulent density flux effects in variable density flow by an explicit algebraic model
- 2015
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Ingår i: Physics of fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 27:4
-
Tidskriftsartikel (refereegranskat)abstract
- The explicit algebraic Reynolds stress model of Grigoriev et al. ["A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation," Phys. Fluids 25, 105112 (2013)] is extended to account for the turbulent density flux in variable density flows. The influence of the mean dilatation and the variation of mean density on the rapid pressure-strain correlation are properly accounted for introducing terms balancing a so-called "baroclinic" production in the Reynolds stress tensor equation. Applying the weak-equilibrium assumption leads to a self-consistent formulation of the model. The model together with a K - ω model is applied to a quasi-one-dimensional plane nozzle flow transcending from subsonic to supersonic regimes. The model remains realizable with constraints put on the model parameters. When density fluxes are taken into account, the model is less likely to become unrealizable. The density variance coupled with a "local mean acceleration" also can influence the model acting to increase anisotropy. The general trends of the behaviour of the anisotropy and production components under the variation of model parameters are assessed. We show how the explicit model can be applied to two- and three-dimensional mean flows without previous knowledge of a tensor basis to obtain the general solution. Approaches are proposed in order to achieve an approximate solution to the consistency equation in cases when analytic solution is missing. In summary, the proposed model has the potential to significantly improve simulations of variable-density flows.
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| 12. |
- Grigoriev, Igor, 1984-, et al.
(författare)
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Algebraic Reynolds stress modeling of turbulence subject to rapid homogeneous and non-homogeneous compression or expansion
- 2016
-
Ingår i: Physics of fluids. - : American Institute of Physics (AIP). - 1070-6631 .- 1089-7666. ; 28:2, s. 026101-
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Tidskriftsartikel (refereegranskat)abstract
- A recently developed explicit algebraic Reynolds stress model (EARSM) by Grigoriev et al. ["A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation," Phys. Fluids 25(10), 105112 (2013)] and the related differential Reynolds stress model (DRSM) are used to investigate the influence of homogeneous shear and compression on the evolution of turbulence in the limit of rapid distortion theory (RDT). The DRSM predictions of the turbulence kinetic energy evolution are in reasonable agreement with RDT while the evolution of diagonal components of anisotropy correctly captures the essential features, which is not the case for standard compressible extensions of DRSMs. The EARSM is shown to give a realizable anisotropy tensor and a correct trend of the growth of turbulence kinetic energy K, which saturates at a power law growth versus compression ratio, as well as retaining a normalized strain in the RDT regime. In contrast, an eddy-viscosity model results in a rapid exponential growth of K and excludes both realizability and high magnitude of the strain rate. We illustrate the importance of using a proper algebraic treatment of EARSM in systems with high values of dilatation and vorticity but low shear. A homogeneously compressed and rotating gas cloud with cylindrical symmetry, related to astrophysical flows and swirling supercritical flows, was investigated too. We also outline the extension of DRSM and EARSM to include the effect of non-homogeneous density coupled with "local mean acceleration" which can be important for, e.g., stratified flows or flows with heat release. A fixed-point analysis of direct numerical simulation data of combustion in a wall-jet flow demonstrates that our model gives quantitatively correct predictions of both streamwise and cross-stream components of turbulent density flux as well as their influence on the anisotropies. In summary, we believe that our approach, based on a proper formulation of the rapid pressure-strain correlation and accounting for the coupling with turbulent density flux, can be an important element in CFD tools for compressible flows.
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| 13. |
- Grigoriev, Igor, 1984-, et al.
(författare)
-
Direct solution for the anisotropy tensor in explicit algebraic Reynolds stress models
- 2016
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- A direct solution to a tensorial equation which constitutes a basis for explicit algebraic Reynolds stress models is derived. We consider equations linear and quasilinear in the strain tensor and show how the independent tensor groups emerge. Solution of an extended model with a linearly coupled active scalar, governed by a linear in anisotropy tensor equation, is also outlined.
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| 14. |
- Grigoriev, Igor, 1984-
(författare)
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Turbulence modeling of compressible flows with large density variation
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this study we highlight the influence of mean dilatation and mean density gradient on the Reynolds stress modeling of compressible, heat-releasing and supercritical turbulent flows.Firstly, the modeling of the rapid pressure-strain correlation has been extended to self-consistently account for the influence of mean dilatation.Secondly, an algebraic model for the turbulent density flux has been developed and coupled to the tensor equationfor Reynolds stress anisotropy via a 'local mean acceleration',a generalization of the buoyancy force.We applied the resulting differential Reynolds stress model (DRSM) and the corresponding explicit algebraic Reynolds stress model (EARSM) to homogeneously sheared and compressed or expanded two-dimensional mean flows. Both formulations have shown that our model preserves the realizability of the turbulence, meaning that the Reynolds stresses do not attain unphysical values, unlike earlier approaches. Comparison with rapid distortion theory (RDT) demonstrated that the DRSM captures the essentials of the transient behaviour of the diagonal anisotropies and gives good predictions of the turbulence kinetic energy.A general three-dimensional solution to the coupled EARSM has been formulated. In the case of turbulent flow in de Laval nozzle we investigated the influence of compressibility effects and demonstrated that the different calibrations lead to different turbulence regimes but with retained realizability. We calibrated our EARSM against a DNS of combustion in a wall-jet flow. Correct predictions of turbulent density fluxes have been achieved and essential features of the anisotropy behaviour have been captured.The proposed calibration keeps the model free of singularities for the cases studied. In addition, we have applied the EARSM to the investigation of supercritical carbon dioxide flow in an annulus. The model correctly captured mean enthalpy, temperature and density as well as the turbulence shear stress. Hence, we consider the model as a useful tool for the analysis of a wide range of compressible flows with large density variation.
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| 15. |
- Grigoriev, Igor, 1984-, et al.
(författare)
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Unified explicit algebraic Reynolds stress model for compressible, heat-releasing and supercritical flowswith large density variation
- 2016
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- An explicit algebraic model (EARSM) for variable denstiy turbulent flow developed by Grigoriev et al. [Phys. Fluids (2015)] is revisited here. We apply it to a quasi one-dimensional nozzle flow, a wall-jet flow with combustion and large density variation and a supercritical flow of carbon dioxide with heat transfer and buoyancy. It is confirmed that the coupling between strong mean density gradient due to high speed, heat release or thermodynamic variations and the 'local mean acceleration' of the flow produces strong turbulent density and heat fluxes, which strongly affect the turbulence. The possible calibration branches are identified and analyzed. We show that a simple and unified calibration of the model gives good predictions for all cases considered. Therefore, the model is a reliable tool for the computation of compressible flows with large density variation.
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| 16. |
- Hage, Hayat, et al.
(författare)
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An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi
- 2023
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Ingår i: Microbial Genomics. - 2057-5858. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Sesquiterpene cyclases (STC) catalyse the cyclization of the C15 molecule farnesyl diphosphate into a vast variety of mono- or polycyclic hydrocarbons and, for a few enzymes, oxygenated structures, with diverse stereogenic centres. The huge diversity in sesquiterpene skeleton structures in nature is primarily the result of the type of cyclization driven by the STC. Despite the phenomenal impact of fungal sesquiterpenes on the ecology of fungi and their potentials for applications, the fungal sesquiterpenome is largely untapped. The identification of fungal STC is generally based on protein sequence similarity with characterized enzymes. This approach has improved our knowledge on STC in a few fungal species, but it has limited success for the discovery of distant sequences. Besides, the tools based on secondary metabolite biosynthesis gene clusters have shown poor performance for terpene cyclases. Here, we used four sets of sequences of fungal STC that catalyse four types of cyclization, and specific amino acid motives to identify phylogenetically related sequences in the genomes of basidiomycetes fungi from the order Polyporales. We validated that four STC genes newly identified from the genome sequence of Leiotrametes menziesii, each classified in a different phylogenetic clade, catalysed a predicted cyclization of farnesyl diphosphate. We built HMM models and searched STC genes in 656 fungal genomes genomes. We identified 5605 STC genes, which were classified in one of the four clades and had a predicted cyclization mechanism. We noticed that the HMM models were more accurate for the prediction of the type of cyclization catalysed by basidiomycete STC than for ascomycete STC.
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| 17. |
- Hensen, Noah, et al.
(författare)
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Genome-scale phylogeny and comparative genomics of the fungal order Sordariales
- 2023
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 189
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Tidskriftsartikel (refereegranskat)abstract
- The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking.In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chae-tomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.
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| 18. |
- Kohler, Annegret, et al.
(författare)
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 176-410
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Tidskriftsartikel (refereegranskat)abstract
- To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
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| 19. |
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| 20. |
- Lewin, Harris A., et al.
(författare)
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The Earth BioGenome Project 2020 : Starting the clock
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 21. |
- Martin, Francis, et al.
(författare)
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The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
- 2008
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 452:7183, s. 7-88
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Tidskriftsartikel (refereegranskat)abstract
- Mycorrhizal symbioses -- the union of roots and soil fungi -- are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate, and montane forests all depend upon ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of 2 ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here, we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-million-base genome assembly contains ~ 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features most notably a battery of effector-type small secreted proteins (SSP) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific proteins likely play a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell walls, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus which enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem in order to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
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| 22. |
- Mock, Thomas, et al.
(författare)
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Multiomics in the central Arctic Ocean for benchmarking biodiversity change
- 2022
-
Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 20:10
-
Tidskriftsartikel (refereegranskat)abstract
- Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.
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| 23. |
- Nagy, László G, et al.
(författare)
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Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities.
- 2015
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 33:4, s. 959-970
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Tidskriftsartikel (refereegranskat)abstract
- Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of 10 saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.
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| 24. |
- Padamsee, Mahajabeen, et al.
(författare)
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The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction
- 2012
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 49:3, s. 217-226
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Tidskriftsartikel (refereegranskat)abstract
- Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic.
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| 25. |
- Piskur, Jure, et al.
(författare)
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The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties.
- 2012
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Ingår i: International Journal of Food Microbiology. - : Elsevier BV. - 0168-1605. ; 157:2, s. 202-209
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Tidskriftsartikel (refereegranskat)abstract
- The yeast Dekkera/Brettanomyces bruxellensis can cause enormous economic losses in wine industry due to production of phenolic off-flavor compounds. D. bruxellensis is a distant relative of baker's yeast Saccharomyces cerevisiae. Nevertheless, these two yeasts are often found in the same habitats and share several food-related traits, such as production of high ethanol levels and ability to grow without oxygen. In some food products, like lambic beer, D. bruxellensis can importantly contribute to flavor development. We determined the 13.4Mb genome sequence of the D. bruxellensis strain Y879 (CBS2499) and deduced the genetic background of several "food-relevant" properties and evolutionary history of this yeast. Surprisingly, we find that this yeast is phylogenetically distant to other food-related yeasts and most related to Pichia (Komagataella) pastoris, which is an aerobic poor ethanol producer. We further show that the D. bruxellensis genome does not contain an excess of lineage specific duplicated genes nor a horizontally transferred URA1 gene, two crucial events that promoted the evolution of the food relevant traits in the S. cerevisiae lineage. However, D. bruxellensis has several independently duplicated ADH and ADH-like genes, which are likely responsible for metabolism of alcohols, including ethanol, and also a range of aromatic compounds.
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| 26. |
- Rineau, F., et al.
(författare)
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Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes
- 2017
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Ingår i: Mycorrhiza. - : Springer Science and Business Media LLC. - 0940-6360 .- 1432-1890. ; 27:4, s. 383-396
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Tidskriftsartikel (refereegranskat)abstract
- Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.
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| 27. |
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| 28. |
- Rosling, Anna, 1974-, et al.
(författare)
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Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis
- 2024
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 25:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid.Results: In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89.Conclusion: Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.
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| 29. |
- Shakhova, Natalia, et al.
(författare)
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Current rates and mechanisms of subsea permafrost degradation in the East Siberian Arctic Shelf
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The rates of subsea permafrost degradation and occurrence of gas-migration pathways are key factors controlling the East Siberian Arctic Shelf (ESAS) methane (CH4) emissions, yet these factors still require assessment. It is thought that after inundation, permafrost-degradation rates would decrease over time and submerged thaw-lake taliks would freeze; therefore, no CH4 release would occur for millennia. Here we present results of the first comprehensive scientific re-drilling to show that subsea permafrost in the near-shore zone of the ESAS has a downward movement of the ice-bonded permafrost table of similar to 14 cm year(-1) over the past 31-32 years. Our data reveal polygonal thermokarst patterns on the seafloor and gas-migration associated with submerged taliks, ice scouring and pockmarks. Knowing the rate and mechanisms of subsea permafrost degradation is a prerequisite to meaningful predictions of near-future CH4 release in the Arctic.
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| 30. |
- Valiollahi Bisheh, Roudabeh, et al.
(författare)
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Electrochemical hydrogen production on a metal-free polymer
- 2019
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Ingår i: Sustainable Energy & Fuels. - : Royal Society of Chemistry. - 2398-4902. ; 3:12, s. 3387-3398
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Tidskriftsartikel (refereegranskat)abstract
- The exploration for true electrocatalytic reactions at organic conducting polymer electrodes, including chemisorption of a reactant and desorption of a product, is receiving renewed interest due to the profound implications it could have on low-cost large area electrochemical energy technology. Here, we finalize the debate about the ability of an organic electrode, more specifically poly(3,4-ethylenedioxythiophene) (PEDOT), to be an electrocatalyst for hydrogen production. This paper proves and covers fundamental studies of the hydrogen evolution reaction (HER) on PEDOT films. Both theory based on DFT (Density Functional Theory) and experimental studies using electrochemical techniques and operando mass spectrometry suggest a Volmer-Heyrovsky mechanism for the actual HER on PEDOT. It is shown that PEDOT reaches an exchange current density comparable to that of metals (i.e. Cu, Ni, and Au) and in addition does not form passivating oxide layers or suffer from chemical corrosion in acidic media. Finally, an electrolyzer stack using the organic polymer electrode demonstrates HER performance in real applications.
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| 31. |
- Vandaele, Ann Carine, et al.
(författare)
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Martian dust storm impact on atmospheric H2O and D/H observed by ExoMars Trace Gas Orbiter
- 2019
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Ingår i: Nature. - : Springer. - 1476-4687 .- 1476-4687 .- 0028-0836. ; 568:7753, s. 521-525
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Global dust storms on Mars are rare1,2 but can affect the Martian atmosphere for several months. They can cause changes in atmospheric dynamics and inflation of the atmosphere3, primarily owing to solar heating of the dust3. In turn, changes in atmospheric dynamics can affect the distribution of atmospheric water vapour, with potential implications for the atmospheric photochemistry and climate on Mars4. Recent observations of the water vapour abundance in the Martian atmosphere during dust storm conditions revealed a high-altitude increase in atmospheric water vapour that was more pronounced at high northern latitudes5,6, as well as a decrease in the water column at low latitudes7,8. Here we present concurrent, high-resolution measurements of dust, water and semiheavy water (HDO) at the onset of a global dust storm, obtained by the NOMAD and ACS instruments onboard the ExoMars Trace Gas Orbiter. We report the vertical distribution of the HDO/H2O ratio (D/H) from the planetary boundary layer up to an altitude of 80 kilometres. Our findings suggest that before the onset of the dust storm, HDO abundances were reduced to levels below detectability at altitudes above 40 kilometres. This decrease in HDO coincided with the presence of water-ice clouds. During the storm, an increase in the abundance of H2O and HDO was observed at altitudes between 40 and 80 kilometres. We propose that these increased abundances may be the result of warmer temperatures during the dust storm causing stronger atmospheric circulation and preventing ice cloud formation, which may confine water vapour to lower altitudes through gravitational fall and subsequent sublimation of ice crystals3. The observed changes in H2O and HDO abundance occurred within a few days during the development of the dust storm, suggesting a fast impact of dust storms on the Martian atmosphere.
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