Next projects B review : May 15 2020 Proposal must be submitted before April 30 2020.
Publications and communications which have benefited of mésocentre resources should contain : « Centre de Calcul Intensif d’Aix-Marseille is acknowledged for granting access to its high performance computing resources. »
Recent publications :
2019 |
Marianthi Karageorgi; Simon C Groen; Fidan Sumbul; Julianne N Pelaez; Kirsten I Verster; Jessica M Aguilar; Amy P Hastings; Susan L Bernstein; Teruyuki Matsunaga; Michael Astourian; Geno Guerra; Felix Rico; Susanne Dobler; Anurag A Agrawal; Noah K Whiteman Genome editing retraces the evolution of toxin resistance in the monarch butterfly Journal Article In: NATURE, 574 (7778), pp. 409+, 2019, ISSN: 0028-0836. @article{ISI:000490988300066, title = {Genome editing retraces the evolution of toxin resistance in the monarch butterfly}, author = {Marianthi Karageorgi and Simon C Groen and Fidan Sumbul and Julianne N Pelaez and Kirsten I Verster and Jessica M Aguilar and Amy P Hastings and Susan L Bernstein and Teruyuki Matsunaga and Michael Astourian and Geno Guerra and Felix Rico and Susanne Dobler and Anurag A Agrawal and Noah K Whiteman}, doi = {10.1038/s41586-019-1610-8}, issn = {0028-0836}, year = {2019}, date = {2019-10-01}, journal = {NATURE}, volume = {574}, number = {7778}, pages = {409+}, publisher = {NATURE PUBLISHING GROUP}, address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}, abstract = {Identifying the genetic mechanisms of adaptation requires the elucidation of links between the evolution of DNA sequence, phenotype, and fitness(1). Convergent evolution can be used as a guide to identify candidate mutations that underlie adaptive traits(2-4), and new genome editing technology is facilitating functional validation of these mutations in whole organisms(1,5). We combined these approaches to study a classic case of convergence in insects from six orders, including the monarch butterfly (Danaus plexippus), that have independently evolved to colonize plants that produce cardiac glycoside toxins(6-11). Many of these insects evolved parallel amino acid substitutions in the alpha-subunit (ATP alpha) of the sodium pump (Na+/K+-ATPase)(7-11), the physiological target of cardiac glycosides(12). Here we describe mutational paths involving three repeatedly changing amino acid sites (111, 119 and 122) in ATP alpha that are associated with cardiac glycoside specialization(13,14). We then performed CRISPR-Cas9 base editing on the native Atp alpha gene in Drosophila melanogaster flies and retraced the mutational path taken across the monarch lineage(11,15). We show in vivo, in vitro and in silico that the path conferred resistance and target-site insensitivity to cardiac glycosides(16), culminating in triple mutant `monarch flies' that were as insensitive to cardiac glycosides as monarch butterflies. `Monarch flies' retained small amounts of cardiac glycosides through metamorphosis, a trait that has been optimized in monarch butterflies to deter predators(17-19.) The order in which the substitutions evolved was explained by amelioration of antagonistic pleiotropy through epistasis(13,14,20-22). Our study illuminates how the monarch butterfly evolved resistance to a class of plant toxins, eventually becoming unpalatable, and changing the nature of species interactions within ecological communities(2,6-11,15,17-19).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Identifying the genetic mechanisms of adaptation requires the elucidation of links between the evolution of DNA sequence, phenotype, and fitness(1). Convergent evolution can be used as a guide to identify candidate mutations that underlie adaptive traits(2-4), and new genome editing technology is facilitating functional validation of these mutations in whole organisms(1,5). We combined these approaches to study a classic case of convergence in insects from six orders, including the monarch butterfly (Danaus plexippus), that have independently evolved to colonize plants that produce cardiac glycoside toxins(6-11). Many of these insects evolved parallel amino acid substitutions in the alpha-subunit (ATP alpha) of the sodium pump (Na+/K+-ATPase)(7-11), the physiological target of cardiac glycosides(12). Here we describe mutational paths involving three repeatedly changing amino acid sites (111, 119 and 122) in ATP alpha that are associated with cardiac glycoside specialization(13,14). We then performed CRISPR-Cas9 base editing on the native Atp alpha gene in Drosophila melanogaster flies and retraced the mutational path taken across the monarch lineage(11,15). We show in vivo, in vitro and in silico that the path conferred resistance and target-site insensitivity to cardiac glycosides(16), culminating in triple mutant `monarch flies' that were as insensitive to cardiac glycosides as monarch butterflies. `Monarch flies' retained small amounts of cardiac glycosides through metamorphosis, a trait that has been optimized in monarch butterflies to deter predators(17-19.) The order in which the substitutions evolved was explained by amelioration of antagonistic pleiotropy through epistasis(13,14,20-22). Our study illuminates how the monarch butterfly evolved resistance to a class of plant toxins, eventually becoming unpalatable, and changing the nature of species interactions within ecological communities(2,6-11,15,17-19). |
Flavio Ronetti; Luca Vannucci; Dario Ferraro; Thibaut Jonckheere; Jér^ome Rech; Thierry Martin; Maura Sassetti Hong-Ou-Mandel heat noise in the quantum Hall regime Journal Article In: Phys. Rev. B, 99 , pp. 205406, 2019. @article{PhysRevB.99.205406, title = {Hong-Ou-Mandel heat noise in the quantum Hall regime}, author = {Flavio Ronetti and Luca Vannucci and Dario Ferraro and Thibaut Jonckheere and Jér^ome Rech and Thierry Martin and Maura Sassetti}, url = {https://link.aps.org/doi/10.1103/PhysRevB.99.205406}, doi = {10.1103/PhysRevB.99.205406}, year = {2019}, date = {2019-05-01}, journal = {Phys. Rev. B}, volume = {99}, pages = {205406}, publisher = {American Physical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pingping Jiang; Pascal Boulet; Marie-Christine Record A DFT study of the electronic, optical and topological properties of free and biaxially strained CuIn1-xAlxSe2 Journal Article In: JOURNAL OF MATERIALS CHEMISTRY C, 7 (19), pp. 5803-5815, 2019, ISSN: 2050-7526. @article{ISI:000472444000028, title = {A DFT study of the electronic, optical and topological properties of free and biaxially strained CuIn1-xAlxSe2}, author = {Pingping Jiang and Pascal Boulet and Marie-Christine Record}, doi = {10.1039/c9tc00277d}, issn = {2050-7526}, year = {2019}, date = {2019-05-01}, journal = {JOURNAL OF MATERIALS CHEMISTRY C}, volume = {7}, number = {19}, pages = {5803-5815}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {The electronic and optical properties of free and biaxially strained CuIn1-xAlxSe2 were calculated by using the full potential linear augmented plane wave (FP-LAPW) method. The results show that CuIn1-xAlxSe2 has a direct band gap with increasing value as x increases. CuIn0.75Al0.25Se2 has been recognized as the optimally substituted compound in terms of band gap and conversion efficiency. The geometry optimized bond length and bond angle between nuclei terminal atoms (M and Se) and the bond critical point, the electron density , the local energy density, and Laplacian delta(2) for nonequivalent pairwise M-Se were examined. High bond deflection with a small bond angle provides a high possibility of electron transition, which mainly occurs between In and Se orbitals. Under biaxial strains, the optical properties are improved along the lengthened deformation direction.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The electronic and optical properties of free and biaxially strained CuIn1-xAlxSe2 were calculated by using the full potential linear augmented plane wave (FP-LAPW) method. The results show that CuIn1-xAlxSe2 has a direct band gap with increasing value as x increases. CuIn0.75Al0.25Se2 has been recognized as the optimally substituted compound in terms of band gap and conversion efficiency. The geometry optimized bond length and bond angle between nuclei terminal atoms (M and Se) and the bond critical point, the electron density , the local energy density, and Laplacian delta(2) for nonequivalent pairwise M-Se were examined. High bond deflection with a small bond angle provides a high possibility of electron transition, which mainly occurs between In and Se orbitals. Under biaxial strains, the optical properties are improved along the lengthened deformation direction. |
S Baschetti; H Bufferand; G Ciraolo; N Fedorczak; P Ghendrih; P Tamain; E Serre; EUROfusion MST1 Team; TCV Team A kappa - epsilon model for plasma anomalous transport in tokamaks: closure via the scaling of the global confinement Journal Article In: NUCLEAR MATERIALS AND ENERGY, 19 , pp. 200-204, 2019. @article{ISI:000470746100032, title = {A kappa - epsilon model for plasma anomalous transport in tokamaks: closure via the scaling of the global confinement}, author = {S Baschetti and H Bufferand and G Ciraolo and N Fedorczak and P Ghendrih and P Tamain and E Serre and EUROfusion MST1 Team and TCV Team}, doi = {10.1016/j.nme.2019.02.032}, year = {2019}, date = {2019-05-01}, journal = {NUCLEAR MATERIALS AND ENERGY}, volume = {19}, pages = {200-204}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {A reduced model for radial anomalous transport of plasma in tokamaks, inspired by the Reynolds-Averaged Navier-Stokes (RANS) approach, is presented assuming diffusion as governing mechanism. In order to self-consistently calculate transport coefficients, an empirical equation is built for the turbulent kinetic energy and the system is closed via the scaling law of global confinement. In such way the SOL width appears to recover experimental dependencies with respect to machine parameters and interestingly, when the model is implemented in a 2D transport code for a realistic study-case, mean fields retrieve some features already observed in 1st-principle turbulent codes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A reduced model for radial anomalous transport of plasma in tokamaks, inspired by the Reynolds-Averaged Navier-Stokes (RANS) approach, is presented assuming diffusion as governing mechanism. In order to self-consistently calculate transport coefficients, an empirical equation is built for the turbulent kinetic energy and the system is closed via the scaling law of global confinement. In such way the SOL width appears to recover experimental dependencies with respect to machine parameters and interestingly, when the model is implemented in a 2D transport code for a realistic study-case, mean fields retrieve some features already observed in 1st-principle turbulent codes. |
J Denis; J Bucalossi; G Ciraolo; E A Hodille; B Pegourie; H Bufferand; C Grisolia; T Loarer; Y Marandet; E Serre; JET Contributors In: NUCLEAR MATERIALS AND ENERGY, 19 , pp. 550-557, 2019. @article{ISI:000470746100086, title = {Dynamic modelling of local fuel inventory and desorption in the whole tokamak vacuum vessel for auto-consistent plasma-wall interaction simulations}, author = {J Denis and J Bucalossi and G Ciraolo and E A Hodille and B Pegourie and H Bufferand and C Grisolia and T Loarer and Y Marandet and E Serre and JET Contributors}, doi = {10.1016/j.nme.2019.03.019}, year = {2019}, date = {2019-05-01}, journal = {NUCLEAR MATERIALS AND ENERGY}, volume = {19}, pages = {550-557}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {An extension of the SolEdge2D-EIRENE code package, named D-WEE, has been developed to add the dynamics of thermal desorption of hydrogen isotopes from the surface of plasma facing materials. To achieve this purpose, D-WEE models hydrogen isotopes implantation, transport and retention in those materials. Before launching autoconsistent simulation (with feedback of D-WEE on SolEdge2D-EIRENE), D-WEE has to be initialised to ensure a realistic wall behaviour in terms of dynamics (pumping or fuelling areas) and fuel content. A methodology based on modelling is introduced to perform such initialisation. A synthetic plasma pulse is built from consecutive SolEdge2D-EIRENE simulations. This synthetic pulse is used as a plasma background for the D-WEE module. A sequence of plasma pulses is simulated with D-WEE to model a tokamak operation. This simulation enables to extract at a desired time during a pulse the local fuel inventory and the local desorption flux density which could be used as initial condition for coupled plasma-wall simulations. To assess the relevance of the dynamic retention behaviour obtained in the simulation, a confrontation to post-pulse experimental pressure measurement is performed. Such confrontation reveals a qualitative agreement between the temporal pressure drop obtained in the simulation and the one observed experimentally. The simulated dynamic retention during the consecutive pulses is also studied.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An extension of the SolEdge2D-EIRENE code package, named D-WEE, has been developed to add the dynamics of thermal desorption of hydrogen isotopes from the surface of plasma facing materials. To achieve this purpose, D-WEE models hydrogen isotopes implantation, transport and retention in those materials. Before launching autoconsistent simulation (with feedback of D-WEE on SolEdge2D-EIRENE), D-WEE has to be initialised to ensure a realistic wall behaviour in terms of dynamics (pumping or fuelling areas) and fuel content. A methodology based on modelling is introduced to perform such initialisation. A synthetic plasma pulse is built from consecutive SolEdge2D-EIRENE simulations. This synthetic pulse is used as a plasma background for the D-WEE module. A sequence of plasma pulses is simulated with D-WEE to model a tokamak operation. This simulation enables to extract at a desired time during a pulse the local fuel inventory and the local desorption flux density which could be used as initial condition for coupled plasma-wall simulations. To assess the relevance of the dynamic retention behaviour obtained in the simulation, a confrontation to post-pulse experimental pressure measurement is performed. Such confrontation reveals a qualitative agreement between the temporal pressure drop obtained in the simulation and the one observed experimentally. The simulated dynamic retention during the consecutive pulses is also studied. |
G Giorgiani; H Bufferand; G Ciraolo; E Serre; P Tamain A magnetic-field independent approach for strongly anisotropic equations arising plasma-edge transport simulations Journal Article In: NUCLEAR MATERIALS AND ENERGY, 19 , pp. 340-345, 2019. @article{ISI:000470746100054, title = {A magnetic-field independent approach for strongly anisotropic equations arising plasma-edge transport simulations}, author = {G Giorgiani and H Bufferand and G Ciraolo and E Serre and P Tamain}, doi = {10.1016/j.nme.2019.03.002}, year = {2019}, date = {2019-05-01}, journal = {NUCLEAR MATERIALS AND ENERGY}, volume = {19}, pages = {340-345}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {A [Summary] The control of the power exhaust in tokamaks is still an open issue for the future fusion operations. The heat loads on divertor and limiter PFCs is largely determined by the physics of the Scrape-Off Layer (SOL), and therefore it depends mainly on the geometry of the magnetic surfaces and on the geometry of wall components. A better characterization of the heat exhaust mechanisms requires therefore to improve the capabilities of the transport codes in terms of geometrical description of the wall components and in terms of the description of the magnetic geometry. The possibility of dealing with evolving magnetic configurations becomes also critical: during start-up or control operations, for example, the evolution of particles and heat fluxes is little known, although being critical for the safety of the machine. Hence, among the new capabilities of future transport codes will be the possibility of accurately describe the reactor chamber, and the flexibility with respect the magnetic configuration. In particular, avoiding expensive re-meshing of the computational domain in case of evolving equilibrium is mandatory. In order to fulfill these requirements, in this work a fluid solver based on non-aligned discretization is used to solve the plasma-edge transport equations for density, momentum and energies. Preliminary tests on non-structured meshes and realistic geometries/physical parameters show the pertinency of this novel approach.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A [Summary] The control of the power exhaust in tokamaks is still an open issue for the future fusion operations. The heat loads on divertor and limiter PFCs is largely determined by the physics of the Scrape-Off Layer (SOL), and therefore it depends mainly on the geometry of the magnetic surfaces and on the geometry of wall components. A better characterization of the heat exhaust mechanisms requires therefore to improve the capabilities of the transport codes in terms of geometrical description of the wall components and in terms of the description of the magnetic geometry. The possibility of dealing with evolving magnetic configurations becomes also critical: during start-up or control operations, for example, the evolution of particles and heat fluxes is little known, although being critical for the safety of the machine. Hence, among the new capabilities of future transport codes will be the possibility of accurately describe the reactor chamber, and the flexibility with respect the magnetic configuration. In particular, avoiding expensive re-meshing of the computational domain in case of evolving equilibrium is mandatory. In order to fulfill these requirements, in this work a fluid solver based on non-aligned discretization is used to solve the plasma-edge transport equations for density, momentum and energies. Preliminary tests on non-structured meshes and realistic geometries/physical parameters show the pertinency of this novel approach. |
B Favier; J Purseed; L Duchemin Rayleigh–Bénard convection with a melting boundary Journal Article In: Journal of Fluid Mechanics, 858 , pp. 437–473, 2019. @article{favier_purseed_duchemin_2019b, title = {Rayleigh–Bénard convection with a melting boundary}, author = {B Favier and J Purseed and L Duchemin}, doi = {10.1017/jfm.2018.773}, year = {2019}, date = {2019-01-01}, journal = {Journal of Fluid Mechanics}, volume = {858}, pages = {437–473}, publisher = {Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hassan Denawi; Mathieu Abel; Roland Hayn Magnetic Polymer Chains of Transition Metal Atoms and Zwitterionic Quinone Journal Article In: The Journal of Physical Chemistry C, 123 (7), pp. 4582-4589, 2019. @article{doi:10.1021/acs.jpcc.8b12433, title = {Magnetic Polymer Chains of Transition Metal Atoms and Zwitterionic Quinone}, author = {Hassan Denawi and Mathieu Abel and Roland Hayn}, url = {https://doi.org/10.1021/acs.jpcc.8b12433}, doi = {10.1021/acs.jpcc.8b12433}, year = {2019}, date = {2019-01-01}, journal = {The Journal of Physical Chemistry C}, volume = {123}, number = {7}, pages = {4582-4589}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
M Valentinuzzi; Y Marandet; H Bufferand; G Ciraolo; P Tamain Two-phases hybrid model for neutrals Journal Article In: Nuclear Materials and Energy, 18 , pp. 41 - 45, 2019, ISSN: 2352-1791. @article{VALENTINUZZI201941, title = {Two-phases hybrid model for neutrals}, author = {M Valentinuzzi and Y Marandet and H Bufferand and G Ciraolo and P Tamain}, url = {http://www.sciencedirect.com/science/article/pii/S2352179118301856}, doi = {https://doi.org/10.1016/j.nme.2018.12.003}, issn = {2352-1791}, year = {2019}, date = {2019-01-01}, journal = {Nuclear Materials and Energy}, volume = {18}, pages = {41 - 45}, abstract = {A new hybrid fluid-kinetic code for the atoms has been developed and implemented in Soledge2D. The new code package is able to simulate the evolution of ions, electrons, molecules and two different populations (or phases) of atoms in realistic 2D geometry. Simulations in ITER geometry show that, with a fluid breakdown parameter of up to 0.1÷0.5, only negligible differences are found with respect to fully-kinetic Soledge2D–Eirene cases, while at the same time improving the computational performances of the code package.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new hybrid fluid-kinetic code for the atoms has been developed and implemented in Soledge2D. The new code package is able to simulate the evolution of ions, electrons, molecules and two different populations (or phases) of atoms in realistic 2D geometry. Simulations in ITER geometry show that, with a fluid breakdown parameter of up to 0.1÷0.5, only negligible differences are found with respect to fully-kinetic Soledge2D–Eirene cases, while at the same time improving the computational performances of the code package. |
D M Fan; Y Marandet; P Tamain; H Bufferand; G Ciraolo; Ph. Ghendrih; E Serre Effect of turbulent fluctuations on neutral particles transport with the TOKAM3X-EIRENE turbulence code Journal Article In: Nuclear Materials and Energy, 18 , pp. 105 - 110, 2019, ISSN: 2352-1791. @article{FAN2019105, title = {Effect of turbulent fluctuations on neutral particles transport with the TOKAM3X-EIRENE turbulence code}, author = {D M Fan and Y Marandet and P Tamain and H Bufferand and G Ciraolo and Ph. Ghendrih and E Serre}, url = {http://www.sciencedirect.com/science/article/pii/S2352179118301200}, doi = {https://doi.org/10.1016/j.nme.2018.12.011}, issn = {2352-1791}, year = {2019}, date = {2019-01-01}, journal = {Nuclear Materials and Energy}, volume = {18}, pages = {105 - 110}, abstract = {The effect of turbulent fluctuations on the transport of neutral particles (atoms, molecules) in tokamak plasmas is investigated with the 3D global turbulence code TOKAM3X-EIRENE in limiter geometry. The statistical properties of turbulent fields relevant to this work are discussed, including the recycling flux. The neutral particle transport is recalculated on the mean field plasma, and compared to the mean neutral particle density/flows obtained from the turbulent simulation, so as to assess the effects of the fluctuations, in particular on the ionization balance. The latter effects are remarkably modest in the simulation presented here, but are expected to become more and more pronounced as the high recycling regime is approached, in particular because the plasma temperature becomes low enough so that ionization is strongly non-linear. However, the turbulent fluctuations in the SOL do have a substantial effect on the neutral densities on the low field side of the limiter, including in the confined plasma. These effects are traced back to non-linearities in the plasma flux at the wall, and the fluctuations in the latter are identified as an important contributor both to neutral particle density fluctuations and to deviations from mean neutral particle density/flows in the turbulent simulation with respect to the same quantities recalculated on the mean plasma fields.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of turbulent fluctuations on the transport of neutral particles (atoms, molecules) in tokamak plasmas is investigated with the 3D global turbulence code TOKAM3X-EIRENE in limiter geometry. The statistical properties of turbulent fields relevant to this work are discussed, including the recycling flux. The neutral particle transport is recalculated on the mean field plasma, and compared to the mean neutral particle density/flows obtained from the turbulent simulation, so as to assess the effects of the fluctuations, in particular on the ionization balance. The latter effects are remarkably modest in the simulation presented here, but are expected to become more and more pronounced as the high recycling regime is approached, in particular because the plasma temperature becomes low enough so that ionization is strongly non-linear. However, the turbulent fluctuations in the SOL do have a substantial effect on the neutral densities on the low field side of the limiter, including in the confined plasma. These effects are traced back to non-linearities in the plasma flux at the wall, and the fluctuations in the latter are identified as an important contributor both to neutral particle density fluctuations and to deviations from mean neutral particle density/flows in the turbulent simulation with respect to the same quantities recalculated on the mean plasma fields. |
F Nespoli; H Bufferand; M Valentinuzzi; N Fedorczak; G Ciraolo; E Serre; Y Marandet; R Maurizio; De H Oliveira; B Labit; M Komm; M Faitsch; S Elmore Application of a two-fluid two-point model to SolEdge2D-EIRENE simulations of TCV H-mode plasma Journal Article In: Nuclear Materials and Energy, 18 , pp. 29 - 34, 2019, ISSN: 2352-1791. @article{NESPOLI201929, title = {Application of a two-fluid two-point model to SolEdge2D-EIRENE simulations of TCV H-mode plasma}, author = {F Nespoli and H Bufferand and M Valentinuzzi and N Fedorczak and G Ciraolo and E Serre and Y Marandet and R Maurizio and De H Oliveira and B Labit and M Komm and M Faitsch and S Elmore}, url = {http://www.sciencedirect.com/science/article/pii/S2352179118301819}, doi = {https://doi.org/10.1016/j.nme.2018.11.026}, issn = {2352-1791}, year = {2019}, date = {2019-01-01}, journal = {Nuclear Materials and Energy}, volume = {18}, pages = {29 - 34}, abstract = {The edge and scrape-off layer (SOL) plasma of the inter-ELM phase of an H-mode discharge from the TCV tokamak is modeled with the transport code SolEdge2D-EIRENE (Bufferand et al. Nuclear Fusion 55 (2015)). The numerical simulations, in presence and in absence of C impurities sputtered from the first wall, are presented and compared with the experiments, finding an overall good agreement. The application of the standard two-point model to the simulation results leads to an apparent momentum gain along the divertor leg. A two-fluid two-point model featuring thermally decoupled ions and electrons is introduced and applied to the simulation results, overcoming this apparent discrepancy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The edge and scrape-off layer (SOL) plasma of the inter-ELM phase of an H-mode discharge from the TCV tokamak is modeled with the transport code SolEdge2D-EIRENE (Bufferand et al. Nuclear Fusion 55 (2015)). The numerical simulations, in presence and in absence of C impurities sputtered from the first wall, are presented and compared with the experiments, finding an overall good agreement. The application of the standard two-point model to the simulation results leads to an apparent momentum gain along the divertor leg. A two-fluid two-point model featuring thermally decoupled ions and electrons is introduced and applied to the simulation results, overcoming this apparent discrepancy. |
H Bufferand; P Tamain; S Baschetti; J Bucalossi; G Ciraolo; N Fedorczak; Ph. Ghendrih; F Nespoli; F Schwander; E Serre; Y Marandet Three-dimensional modelling of edge multi-component plasma taking into account realistic wall geometry Journal Article In: Nuclear Materials and Energy, 18 , pp. 82 - 86, 2019, ISSN: 2352-1791. @article{BUFFERAND201982, title = {Three-dimensional modelling of edge multi-component plasma taking into account realistic wall geometry}, author = {H Bufferand and P Tamain and S Baschetti and J Bucalossi and G Ciraolo and N Fedorczak and Ph. Ghendrih and F Nespoli and F Schwander and E Serre and Y Marandet}, url = {http://www.sciencedirect.com/science/article/pii/S2352179118302035}, doi = {https://doi.org/10.1016/j.nme.2018.11.025}, issn = {2352-1791}, year = {2019}, date = {2019-01-01}, journal = {Nuclear Materials and Energy}, volume = {18}, pages = {82 - 86}, abstract = {A 3D multispecies fluid model has been implemented in the SOLEDGE-TOKAM suite of codes to address Scrape-off layer turbulent impurity transport. Zhdanov closure is used to address multi-component plasma modeling without any mass ordering or trace impurity assumption. Thanks to immersed boundary conditions, up to the wall simulations with non-axisymmetric plasma facing components are performed, in particular in the WEST configuration. A first proof of principle of interchange turbulence simulation of a Deuterium+Carbon plasma is also reported.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A 3D multispecies fluid model has been implemented in the SOLEDGE-TOKAM suite of codes to address Scrape-off layer turbulent impurity transport. Zhdanov closure is used to address multi-component plasma modeling without any mass ordering or trace impurity assumption. Thanks to immersed boundary conditions, up to the wall simulations with non-axisymmetric plasma facing components are performed, in particular in the WEST configuration. A first proof of principle of interchange turbulence simulation of a Deuterium+Carbon plasma is also reported. |
Cédric Maury; Teresa Bravo; Daniel Mazzoni The use of microperforations to attenuate the cavity pressure fluctuations induced by a low-speed flow Journal Article In: Journal of Sound and Vibration, 439 , pp. 1 - 16, 2019, ISSN: 0022-460X. @article{MAURY20191, title = {The use of microperforations to attenuate the cavity pressure fluctuations induced by a low-speed flow}, author = {Cédric Maury and Teresa Bravo and Daniel Mazzoni}, url = {http://www.sciencedirect.com/science/article/pii/S0022460X18306400}, doi = {https://doi.org/10.1016/j.jsv.2018.09.045}, issn = {0022-460X}, year = {2019}, date = {2019-01-01}, journal = {Journal of Sound and Vibration}, volume = {439}, pages = {1 - 16}, abstract = {The paper describes experimental and numerical studies on the use of micro-perforated panels to reduce the flow cavity pressure fluctuations under a low-speed turbulent boundary layer. This passive strategy has been hardly studied in shallow cavities with length-to-depth ratios of the order of 10, for which flow reattachment might occur at the cavity floor. This implies the formation of a localized recirculation bubble upstream in the cavity, which is referred to as a closed cavity flow regime. An open flow regime takes place when the cavity is separated from the main flow by a shear layer over the full length. For a transitional case with a length-to-depth ratio of 10.6, micro-perforating the cavity floor reduces by up to 8 dB the dominant spectral peaks related to the bottom wall-pressure fluctuations in the first half of the cavity. For the closed regime with a length-to-depth ratio of 17.6, up to 6 dB reduction is found. The broadband fluctuations that are dominating in the downstream part of the cavity are not affected by the presence of the micro-perforations. Reduction of the peak pressure levels by the apertures is confirmed by two-dimensional Lattice Boltzmann simulations. Maximum dissipation occurs when outflow conditions are established within and at the inlet-outlet of the orifices. The impedance of the micro-perforated floor has been optimised and its effect on the bottom wall-pressures has been assessed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The paper describes experimental and numerical studies on the use of micro-perforated panels to reduce the flow cavity pressure fluctuations under a low-speed turbulent boundary layer. This passive strategy has been hardly studied in shallow cavities with length-to-depth ratios of the order of 10, for which flow reattachment might occur at the cavity floor. This implies the formation of a localized recirculation bubble upstream in the cavity, which is referred to as a closed cavity flow regime. An open flow regime takes place when the cavity is separated from the main flow by a shear layer over the full length. For a transitional case with a length-to-depth ratio of 10.6, micro-perforating the cavity floor reduces by up to 8 dB the dominant spectral peaks related to the bottom wall-pressure fluctuations in the first half of the cavity. For the closed regime with a length-to-depth ratio of 17.6, up to 6 dB reduction is found. The broadband fluctuations that are dominating in the downstream part of the cavity are not affected by the presence of the micro-perforations. Reduction of the peak pressure levels by the apertures is confirmed by two-dimensional Lattice Boltzmann simulations. Maximum dissipation occurs when outflow conditions are established within and at the inlet-outlet of the orifices. The impedance of the micro-perforated floor has been optimised and its effect on the bottom wall-pressures has been assessed. |
Christine D Wilson; Laura C Parker; Ryan Chown; Niu Li; Cheng Li; Houjun Mo; E Athanassoula; Lin Lin; Ting Xiao Linking bar- and interaction-driven molecular gas concentration with centrally enhanced star formation in EDGE–CALIFA galaxies Journal Article In: Monthly Notices of the Royal Astronomical Society, 484 (4), pp. 5192-5211, 2019, ISSN: 0035-8711. @article{10.1093/mnras/stz349, title = {Linking bar- and interaction-driven molecular gas concentration with centrally enhanced star formation in EDGE–CALIFA galaxies}, author = {Christine D Wilson and Laura C Parker and Ryan Chown and Niu Li and Cheng Li and Houjun Mo and E Athanassoula and Lin Lin and Ting Xiao}, url = {https://doi.org/10.1093/mnras/stz349}, doi = {10.1093/mnras/stz349}, issn = {0035-8711}, year = {2019}, date = {2019-01-01}, journal = {Monthly Notices of the Royal Astronomical Society}, volume = {484}, number = {4}, pages = {5192-5211}, abstract = {We study the spatially resolved star formation history (SFH) and molecular gas distribution of 58 nearby galaxies, using integral field spectroscopy from the CALIFA survey and CO J = 1–0 intensity mapping from the CARMA EDGE survey. We use the 4000 Å break (Dn(4000)), the equivalent width (EW) of the H δ absorption line (EW(H δA)), and the EW of the H α emission line (EW(H α)) to measure the recent SFH of these galaxies. We measure radial profiles of the three SFH indicators and molecular gas mass surface density, from which we measure the level of centrally enhanced star formation and the molecular gas concentration. When we separate our galaxies into categories of barred (17 galaxies), unbarred (24 galaxies), and merging/paired (17 galaxies), we find that the galaxies that have centrally enhanced star formation (19/58) are either barred (13/19) or in mergers/pairs (6/19) with relatively high molecular gas concentrations. A comparison between our barred galaxies and a snapshot of a hydrodynamic N-body simulation of a barred galaxy shows that the current theory of bar formation and evolution can qualitatively reproduce the main features of the observed galaxies in our sample, including both the sharp decrease of stellar age in the galactic centre and the gradual decrease of age with increasing distance from centre. These findings provide substantial evidence for a picture in which cold gas is transported inwards by a bar or tidal interaction, which leads to the growth and rejuvenation of star formation in the central region.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study the spatially resolved star formation history (SFH) and molecular gas distribution of 58 nearby galaxies, using integral field spectroscopy from the CALIFA survey and CO J = 1–0 intensity mapping from the CARMA EDGE survey. We use the 4000 Å break (Dn(4000)), the equivalent width (EW) of the H δ absorption line (EW(H δA)), and the EW of the H α emission line (EW(H α)) to measure the recent SFH of these galaxies. We measure radial profiles of the three SFH indicators and molecular gas mass surface density, from which we measure the level of centrally enhanced star formation and the molecular gas concentration. When we separate our galaxies into categories of barred (17 galaxies), unbarred (24 galaxies), and merging/paired (17 galaxies), we find that the galaxies that have centrally enhanced star formation (19/58) are either barred (13/19) or in mergers/pairs (6/19) with relatively high molecular gas concentrations. A comparison between our barred galaxies and a snapshot of a hydrodynamic N-body simulation of a barred galaxy shows that the current theory of bar formation and evolution can qualitatively reproduce the main features of the observed galaxies in our sample, including both the sharp decrease of stellar age in the galactic centre and the gradual decrease of age with increasing distance from centre. These findings provide substantial evidence for a picture in which cold gas is transported inwards by a bar or tidal interaction, which leads to the growth and rejuvenation of star formation in the central region. |
Ran Liu; Xing Gao; Mario Barbatti; Jun Jiang; Guozhen Zhang Promoting Intersystem Crossing of a Fluorescent Molecule via Single Functional Group Modification Journal Article In: The Journal of Physical Chemistry Letters, 10 (6), pp. 1388-1393, 2019. @article{doi:10.1021/acs.jpclett.9b00286, title = {Promoting Intersystem Crossing of a Fluorescent Molecule via Single Functional Group Modification}, author = {Ran Liu and Xing Gao and Mario Barbatti and Jun Jiang and Guozhen Zhang}, url = {https://doi.org/10.1021/acs.jpclett.9b00286}, doi = {10.1021/acs.jpclett.9b00286}, year = {2019}, date = {2019-01-01}, journal = {The Journal of Physical Chemistry Letters}, volume = {10}, number = {6}, pages = {1388-1393}, abstract = {Pure light-atom organic phosphorescent molecules have been under scientific scrutiny because they are inexpensive, flexible, and environment friendly. The development of such materials, however, faces a bottleneck problem of intrinsically small spin–orbit couplings, which can be addressed by seeking a proper balance between intersystem crossing (ISC) and fluorescence rates. Using N-substituted naphthalimides as the prototype molecule, we applied chemical modifications with several electrophilic and nucleophilic functional groups, to approach the goal. The selected electron donating groups actively restrain the fluorescence, enabling an efficient ISC to the triplet manifold. Electron withdrawing groups do not change the luminescent properties of the parent species. The changes in ISC and fluorescence rates are related to the nature of the lowest singlet state, which changes from localized excitation into charge-transfer excitation upon configuration change of excited molecules. This finding opens an alternative strategy for designing pure light-atom organic phosphorescent molecules for emerging luminescent materials applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Pure light-atom organic phosphorescent molecules have been under scientific scrutiny because they are inexpensive, flexible, and environment friendly. The development of such materials, however, faces a bottleneck problem of intrinsically small spin–orbit couplings, which can be addressed by seeking a proper balance between intersystem crossing (ISC) and fluorescence rates. Using N-substituted naphthalimides as the prototype molecule, we applied chemical modifications with several electrophilic and nucleophilic functional groups, to approach the goal. The selected electron donating groups actively restrain the fluorescence, enabling an efficient ISC to the triplet manifold. Electron withdrawing groups do not change the luminescent properties of the parent species. The changes in ISC and fluorescence rates are related to the nature of the lowest singlet state, which changes from localized excitation into charge-transfer excitation upon configuration change of excited molecules. This finding opens an alternative strategy for designing pure light-atom organic phosphorescent molecules for emerging luminescent materials applications. |
Gessenildo Pereira Rodrigues; Thayana Maria Lopes de Lima; Railton Barbosa de Andrade; Elizete Ventura; Silmar Andrade do Monte; Mario Barbatti Photoinduced Formation of H-Bonded Ion Pair in HCFC-133a Journal Article In: The Journal of Physical Chemistry A, 123 (10), pp. 1953-1961, 2019, (PMID: 30786711). @article{doi:10.1021/acs.jpca.8b12482, title = {Photoinduced Formation of H-Bonded Ion Pair in HCFC-133a}, author = {Gessenildo Pereira Rodrigues and Thayana Maria Lopes de Lima and Railton Barbosa de Andrade and Elizete Ventura and Silmar Andrade do Monte and Mario Barbatti}, url = {https://doi.org/10.1021/acs.jpca.8b12482}, doi = {10.1021/acs.jpca.8b12482}, year = {2019}, date = {2019-01-01}, journal = {The Journal of Physical Chemistry A}, volume = {123}, number = {10}, pages = {1953-1961}, abstract = {High-level multireference electronic structure calculations have been performed to study the Cl– yield from photoexcited CF3CH2Cl (HCFC-133a). The analysis of this process tells that it relates to an electron transfer from the carbon to the Cl atom, forming a highly polar contact ion-pair complex, CF3HCH+···Cl–, in the excited (S3) state. This complex has a strong binding energy of 3.53 eV, from which 0.47 eV is due to an underlying hydrogen bond. Through comparison with the results obtained for the prototype CH3Cl system, where a similar ion-pair state associated with Cl– formation has also been observed, it is suggested that photodissociation of HCFC-133a can also yield Cl– through an analogous process. This hypothesis is further supported by nonadiabatic dynamics simulations, which shows formation of the ion-pair complex in the subpicosecond time scale.}, note = {PMID: 30786711}, keywords = {}, pubstate = {published}, tppubtype = {article} } High-level multireference electronic structure calculations have been performed to study the Cl– yield from photoexcited CF3CH2Cl (HCFC-133a). The analysis of this process tells that it relates to an electron transfer from the carbon to the Cl atom, forming a highly polar contact ion-pair complex, CF3HCH+···Cl–, in the excited (S3) state. This complex has a strong binding energy of 3.53 eV, from which 0.47 eV is due to an underlying hydrogen bond. Through comparison with the results obtained for the prototype CH3Cl system, where a similar ion-pair state associated with Cl– formation has also been observed, it is suggested that photodissociation of HCFC-133a can also yield Cl– through an analogous process. This hypothesis is further supported by nonadiabatic dynamics simulations, which shows formation of the ion-pair complex in the subpicosecond time scale. |
Shuming Bai; Mario Barbatti Mechanism of Spin-Exchange Internal Conversion: Practical Proxies for Diabatic and Nonadiabatic Couplings Journal Article In: Journal of Chemical Theory and Computation, 15 (3), pp. 1503-1513, 2019, (PMID: 30735372). @article{doi:10.1021/acs.jctc.8b00923, title = {Mechanism of Spin-Exchange Internal Conversion: Practical Proxies for Diabatic and Nonadiabatic Couplings}, author = {Shuming Bai and Mario Barbatti}, url = {https://doi.org/10.1021/acs.jctc.8b00923}, doi = {10.1021/acs.jctc.8b00923}, year = {2019}, date = {2019-01-01}, journal = {Journal of Chemical Theory and Computation}, volume = {15}, number = {3}, pages = {1503-1513}, abstract = {Spin-exchange internal conversion (SEIC) is a general class of reactions having singlet fission and triplet fusion as particular cases. Based on a charge transfer (CT) mediated mechanism and analytical derivation with a model Hamiltonian, we propose proxies for estimating the coupling strength in both diabatic and adiabatic pictures for general SEIC reactions. In the diabatic picture, we demonstrated the existence of a bilinear relationship between the coupling strength and molecular orbital overlap, which provides a practical way to predict diabatic couplings. In the adiabatic picture, we showed that nonadiabatic couplings can be approximated by simple functions of the wave function CT coefficients. These approaches were verified through the investigation of singlet oxygen photosensitization, where both 1Δg and 1Σg oxygen states can be competitively generated by a triplet fusion reaction. The interplay between the CT-mediated mechanism, the spatial factors of the bimolecular complex, and the electronic structure of the oxygen molecule during the reaction explains the curiously small coupling to the 1Σg state along specific incidence directions. The results from both the diabatic and adiabatic pictures provide a comprehensive understanding of the reaction mechanism, which applies to general SEIC problems.}, note = {PMID: 30735372}, keywords = {}, pubstate = {published}, tppubtype = {article} } Spin-exchange internal conversion (SEIC) is a general class of reactions having singlet fission and triplet fusion as particular cases. Based on a charge transfer (CT) mediated mechanism and analytical derivation with a model Hamiltonian, we propose proxies for estimating the coupling strength in both diabatic and adiabatic pictures for general SEIC reactions. In the diabatic picture, we demonstrated the existence of a bilinear relationship between the coupling strength and molecular orbital overlap, which provides a practical way to predict diabatic couplings. In the adiabatic picture, we showed that nonadiabatic couplings can be approximated by simple functions of the wave function CT coefficients. These approaches were verified through the investigation of singlet oxygen photosensitization, where both 1Δg and 1Σg oxygen states can be competitively generated by a triplet fusion reaction. The interplay between the CT-mediated mechanism, the spatial factors of the bimolecular complex, and the electronic structure of the oxygen molecule during the reaction explains the curiously small coupling to the 1Σg state along specific incidence directions. The results from both the diabatic and adiabatic pictures provide a comprehensive understanding of the reaction mechanism, which applies to general SEIC problems. |
Pierre Thureau; Simone Sturniolo; Miri Zilka; Fabio Ziarelli; Stéphane Viel; Jonathan R Yates; Giulia Mollica In: Magnetic Resonance in Chemistry, 57 (5), pp. 256-264, 2019. @article{doi:10.1002/mrc.4848, title = {Reducing the computational cost of NMR crystallography of organic powders at natural isotopic abundance with the help of 13C-13C dipolar couplings}, author = {Pierre Thureau and Simone Sturniolo and Miri Zilka and Fabio Ziarelli and Stéphane Viel and Jonathan R Yates and Giulia Mollica}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mrc.4848}, doi = {10.1002/mrc.4848}, year = {2019}, date = {2019-01-01}, journal = {Magnetic Resonance in Chemistry}, volume = {57}, number = {5}, pages = {256-264}, abstract = {Abstract Structure determination of functional organic compounds remains a formidable challenge when the sample exists as a powder. Nuclear magnetic resonance crystallography approaches based on the comparison of experimental and Density Functional Theory (DFT)-computed 1H chemical shifts have already demonstrated great potential for structure determination of organic powders, but limitations still persist. In this study, we discuss the possibility of using 13C-13C dipolar couplings quantified on powdered theophylline at natural isotopic abundance with the help of dynamic nuclear polarization, to realize a DFT-free, rapid screening of a pool of structures predicted by ab initio random structure search. We show that although 13C-13C dipolar couplings can identify structures possessing long range structural motifs and unit cell parameters close to those of the true structure, it must be complemented with other data to recover information about the presence and the chemical nature of the supramolecular interactions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Structure determination of functional organic compounds remains a formidable challenge when the sample exists as a powder. Nuclear magnetic resonance crystallography approaches based on the comparison of experimental and Density Functional Theory (DFT)-computed 1H chemical shifts have already demonstrated great potential for structure determination of organic powders, but limitations still persist. In this study, we discuss the possibility of using 13C-13C dipolar couplings quantified on powdered theophylline at natural isotopic abundance with the help of dynamic nuclear polarization, to realize a DFT-free, rapid screening of a pool of structures predicted by ab initio random structure search. We show that although 13C-13C dipolar couplings can identify structures possessing long range structural motifs and unit cell parameters close to those of the true structure, it must be complemented with other data to recover information about the presence and the chemical nature of the supramolecular interactions. |
