@article{Bonfrate2024,

title = {Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators},

author = {Simone Bonfrate and Nicolas Ferré and Miquel Huix-Rotllant},

doi = {10.1021/acs.jctc.4c00201},

issn = {1549-9626},

year  = {2024},

date = {2024-05-28},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {10},

pages = {4338--4349},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Diao2024,

title = {Light-Induced Reactivity Switch at O_{2}–Activating Bioinspired Copper(I) Complexes},

author = {Donglin Diao and Anna Baidiuk and Leo Chaussy and Iago De Assis Modenez and Xavi Ribas and Marius Réglier and Vlad Martin-Diaconescu and Paola Nava and A. Jalila Simaan and Alexandre Martinez and Cédric Colomban},

doi = {10.1021/jacsau.4c00184},

issn = {2691-3704},

year  = {2024},

date = {2024-05-27},

journal = {JACS Au},

volume = {4},

number = {5},

pages = {1966--1974},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chaussy2024,

title = {Spectroscopy of End-On Copper(II) Superoxido Complexes: A Wave Function-Based Analysis},

author = {Léo Chaussy and Vijay Gopal Chilkuri and Stéphane Humbel and Paola Nava},

doi = {10.1021/acs.inorgchem.3c04401},

issn = {1520-510X},

year  = {2024},

date = {2024-05-06},

journal = {Inorg. Chem.},

volume = {63},

number = {18},

pages = {8038--8049},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chou2024,

title = {Atropisomeric N‐Heterocyclic Carbene‐Palladium(II) Complexes: Influence of the Backbone Substitution},

author = {Yajie Chou and Mathilde Vançon and Muriel Albalat and Carla Deschodt and Paola Nava and Stéphane Humbel and Nicolas Vanthuyne and Hervé Clavier},

doi = {10.1002/ejic.202300780},

issn = {1099-0682},

year  = {2024},

date = {2024-04-22},

journal = {Eur J Inorg Chem},

volume = {27},

number = {12},

publisher = {Wiley},

abstract = {AbstractIn order to facilitate the synthesis of NHC precursors as well as to incorporate new moieties, the influence of the NHC backbone substitution was investigated within the concept of atropisomeric NHC‐metal complexes. A series of NHC precursors was prepared from new anilines and used to synthesize the corresponding Pd(allyl)Cl(NHC) complexes, most of the time as a mixture of diastereomers (meso and chiral). Chiral HPLC at preparative scale enabled to obtain enantiopure complexes in low to excellent yields. These complexes displayed good activity in the intramolecular α‐arylation of amides and, as a function of the structure of the chiral catalyst, excellent enantioselectivities were reached (up to 96 % ee).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mukherjee2024,

title = {Prediction Challenge: Simulating Rydberg photoexcited cyclobutanone with surface hopping dynamics based on different electronic structure methods},

author = {Saikat Mukherjee and Rafael S. Mattos and Josene M. Toldo and Hans Lischka and Mario Barbatti},

doi = {10.1063/5.0203636},

issn = {1089-7690},

year  = {2024},

date = {2024-04-21},

volume = {160},

number = {15},

publisher = {AIP Publishing},

abstract = {This research examines the nonadiabatic dynamics of cyclobutanone after excitation into the n → 3s Rydberg S2 state. It stems from our contribution to the Special Topic of the Journal of Chemical Physics to test the predictive capability of computational chemistry against unseen experimental data. Decoherence-corrected fewest-switches surface hopping was used to simulate nonadiabatic dynamics with full and approximated nonadiabatic couplings. Several simulation sets were computed with different electronic structure methods, including a multiconfigurational wavefunction [multiconfigurational self-consistent field (MCSCF)] specially built to describe dissociative channels, multireference semiempirical approach, time-dependent density functional theory, algebraic diagrammatic construction, and coupled cluster. MCSCF dynamics predicts a slow deactivation of the S2 state (10 ps), followed by an ultrafast population transfer from S1 to S0 (<100 fs). CO elimination (C3 channel) dominates over C2H4 formation (C2 channel). These findings radically differ from the other methods, which predicted S2 lifetimes 10–250 times shorter and C2 channel predominance. These results suggest that routine electronic structure methods may hold low predictive power for the outcome of nonadiabatic dynamics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bizet2024,

title = {Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non‐canonical amino acid},

author = {Maxime Bizet and Deborah Byrne and Frédéric Biaso and Guillaume Gerbaud and Emilien Etienne and Giuseppina Briola and Bruno Guigliarelli and Philippe Urban and Pierre Dorlet and Tamas Kalai and Gilles Truan and Marlène Martinho},

doi = {10.1002/chem.202304307},

issn = {1521-3765},

year  = {2024},

date = {2024-04-02},

journal = {Chemistry A European J},

volume = {30},

number = {19},

publisher = {Wiley},

abstract = {AbstractThe flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a “locked/closed” to an “unlocked/open” state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site‐Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non‐canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration‐dependent distance distribution, evidence of an “open” CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the “open” semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hodille2024,

title = {Deuterium uptake, desorption and sputtering from W(110) surface covered with oxygen},

author = {E.A. Hodille and B. Pavec and J. Denis and A. Dunand and Y. Ferro and M. Minissale and T. Angot and C. Grisolia and R. Bisson},

doi = {10.1088/1741-4326/ad2a29},

issn = {1741-4326},

year  = {2024},

date = {2024-04-01},

journal = {Nucl. Fusion},

volume = {64},

number = {4},

publisher = {IOP Publishing},

abstract = {Abstract

               Rate equation modelling is performed to simulate 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                     

                   and 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                        +

                        

                           

                              

                                 D

                              

                              2

                              +

                           

                        

                     

                   exposure of the 

                     

                     

                        

                           

                              W

                           

                           (

                           110

                           )

                        

                     

                   surface with varying coverage of oxygen atoms (O) from the clean surface up to 0.75 monolayer of O. Density Functional Theory (DFT) calculated energetics are used as inputs for the surface processes and desorption energies are optimized to best reproduce the Thermal Desorption Spectrometry (TDS) experiments obtained for 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                     

                   exposure. For the clean surface, the optimized desorption energies (1.10 eV–1.40 eV) are below the DFT ones (1.30 eV–1.50 eV). For the O covered surface, the main desorption peak is reproduced with desorption energies of 1.10 eV and 1.00 eV for 0.50 and 0.75 monolayer of O respectively. This is slightly higher than the DFT predicted desorption energies. In order to simulate satisfactorily the total retention obtained experimentally for 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                        +

                        

                           

                              

                                 D

                              

                              2

                              +

                           

                        

                     

                   exposure, a sputtering process needs to be added to the model, describing the sputtering of adsorbed species (D atoms) by the incident D ions. The impact of the sputtering process on the shape of the TDS spectra, on the total retention and on the recycling of D from the wall is discussed. In order to better characterize the sputtering process, especially its products and yields, atomistic calculations such as molecular dynamics are suggested as a next step for this study.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lin2024,

title = {Synthesizing impurity clustering in the edge plasma of tokamaks using neural networks},

author = {Zetao Lin and Thibault Maurel-Oujia and Benjamin Kadoch and Philipp Krah and Nathaniel Saura and Sadruddin Benkadda and Kai Schneider},

doi = {10.1063/5.0178085},

issn = {1089-7674},

year  = {2024},

date = {2024-03-01},

volume = {31},

number = {3},

publisher = {AIP Publishing},

abstract = {This work investigates the behavior of impurities in edge plasma of tokamaks using high-resolution numerical simulations based on Hasegawa–Wakatani equations. Specifically, it focuses on the behavior of inertial particles, which has not been extensively studied in the field of plasma physics. Our simulations utilize one-way coupling of a large number of inertial point particles, which model plasma impurities. We observe that with Stokes number (St), which characterizes the inertia of particles being much less than one, such light impurities closely track the fluid flow without pronounced clustering. For intermediate St values, distinct clustering appears, with larger Stokes values, i.e., heavy impurities even generating more substantial clusters. When St is significantly large, very heavy impurities tend to detach from the flow and maintain their trajectory, resulting in fewer observable clusters and corresponding to random motion. A core component of this work involves machine learning techniques. Applying three different neural networks—Autoencoder, U-Net, and Generative Adversarial Network (GAN)—to synthesize preferential concentration fields of impurities, we use vorticity as input and predict impurity number density fields. GAN outperforms the two others by aligning closely with direct numerical simulation data in terms of probability density functions of the particle distribution and energy spectra. This machine learning technique holds the potential to reduce computational costs by eliminating the need to track millions of particles modeling impurities in simulations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ma2024,

title = {An averaged mass correction scheme for the simulation of high subsonic turbulent internal flows using a lattice Boltzmann method},

author = {Jingtao Ma and Lincheng Xu and Jérôme Jacob and Eric Serre and Pierre Sagaut},

doi = {10.1063/5.0192360},

issn = {1089-7666},

year  = {2024},

date = {2024-03-01},

volume = {36},

number = {3},

publisher = {AIP Publishing},

abstract = {This paper addresses the simulation of internal high-speed turbulent compressible flows using lattice Boltzmann method (LBM) when it is coupled with the immersed boundary method for non-body-fitted meshes. The focus is made here on the mass leakage issue. The recent LBM pressure-based algorithm [Farag et al. Phys. Fluids 32, 066106 (2020)] has shown its superiority on classical density-based algorithm to simulate high-speed compressible flows. Following our previous theoretical work on incompressible flows [Xu et al. Phys. Fluids 34, 065113 (2022)], we propose an averaged mass correction technique to mitigate mass leakage when simulating high-Mach-number compressible flows. It is adapted to deal here with a density, which is decoupled from the zero-moment definition. The simulations focus on two generic but canonical configurations of more complex industrial devices, the straight channel at different angles of inclination at Mach numbers (Ma) ranging from 0.2 to 0.8, and the National Aeronautics and Space Administration Glenn S-duct at Ma = 0.6. The present results show that mass leakage can be a critical issue for the accuracy of the solution and that the proposed correction technique effectively mitigates it and leads to significant improvements in the prediction of the solution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lazarotto2024,

title = {Island myriads in periodic potentials},

author = {Matheus J. Lazarotto and Iberê L. Caldas and Yves Elskens},

doi = {10.1063/5.0185891},

issn = {1089-7682},

year  = {2024},

date = {2024-03-01},

volume = {34},

number = {3},

publisher = {AIP Publishing},

abstract = {A phenomenon of emergence of stability islands in phase space is reported for two periodic potentials with tiling symmetries, one square and the other hexagonal, inspired by bidimensional Hamiltonian models of optical lattices. The structures found, here termed as island myriads, resemble web-tori with notable fractality and arise at energy levels reaching that of unstable equilibria. In general, the myriad is an arrangement of concentric island chains with properties relying on the translational and rotational symmetries of the potential functions. In the square system, orbits within the myriad come in isochronous pairs and can have different periodic closure, either returning to their initial position or jumping to identical sites in neighbor cells of the lattice, therefore impacting transport properties. As seen when compared to a more generic case, i.e., the rectangular lattice, the breaking of square symmetry disrupts the myriad even for small deviations from its equilateral configuration. For the hexagonal case, the myriad was found but in attenuated form, mostly due to extra instabilities in the potential surface that prevent the stabilization of orbits forming the chains.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dral2024,

title = {MLatom 3: A Platform for Machine Learning-Enhanced Computational Chemistry Simulations and Workflows},

author = {Pavlo O. Dral and Fuchun Ge and Yi-Fan Hou and Peikun Zheng and Yuxinxin Chen and Mario Barbatti and Olexandr Isayev and Cheng Wang and Bao-Xin Xue and Max Pinheiro Jr and Yuming Su and Yiheng Dai and Yangtao Chen and Lina Zhang and Shuang Zhang and Arif Ullah and Quanhao Zhang and Yanchi Ou},

doi = {10.1021/acs.jctc.3c01203},

issn = {1549-9626},

year  = {2024},

date = {2024-02-13},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {3},

pages = {1193--1213},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sartoretto2024,

title = {Ecological and genomic characterization of a remarkable natural heritage: a mesophotic ‘giant’ Paramuricea clavata forest},

author = {S Sartoretto and JB Ledoux and E Gueret and D Guillemain and C Ravel and L Moirand and D Aurelle},

doi = {10.3354/meps14427},

issn = {1616-1599},

year  = {2024},

date = {2024-02-08},

journal = {Mar. Ecol. Prog. Ser.},

volume = {728},

pages = {85--101},

publisher = {Inter-Research Science Center},

abstract = {Paramuricea clavata is an ecosystem engineer, structuring hard bottom communities in the Mediterranean Sea, from 10 to 200 m depth. For more than 2 decades, shallow populations of P. clavata have been impacted by marine heatwaves, resulting in massive mortality events. Recently, a new dense population characterized by the tallest colonies ever recorded (up to 1.80 m) in the Mediterranean Sea was discovered between 50 and 60 m depth. Here, we analyzed the size and genetic structure of this ‘deep giant population’ and conducted a reciprocal transplant experiment with a shallow population inhabiting the same area to test for local adaptation. The experiment showed no significant difference in the survival rate despite the high temperatures registered in the shallow area. Nevertheless, we observed a significant differentiation by depth in this area, with low estimates of gene flow. The particular local oceanographic conditions could lead to a relative isolation of the population. In conclusion, the reduced connectivity of this newly discovered giant population with shallower ones questions its potential role as a climate refuge. Additionally, this population constitutes a unique natural heritage site that should be effectively protected from physical impacts and other direct consequences of anthropogenic activities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Miton2023,

title = {A Cyclotriveratrylene Solvent‐Dependent Chiral Switch},

author = {Louise Miton and Élise Antonetti and Diego García‐López and Paola Nava and Vincent Robert and Muriel Albalat and Nicolas Vanthuyne and Alexandre Martinez and Yoann Cotelle},

doi = {10.1002/chem.202303294},

issn = {1521-3765},

year  = {2024},

date = {2024-02-07},

journal = {Chemistry A European J},

volume = {30},

number = {8},

publisher = {Wiley},

abstract = {AbstractChiral molecular switches are attracting attention as they could pave the way to chiral molecular machines. Herein, we report on the design and synthesis of a single molecule chiral switch based on a cyclotriveratrylene scaffold, in which the chirality inversion is controlled by the solvent. Hemicryptophanes are built around a C3 cyclotriveratrylene chiral unit, with either M or P handedness, connected to another tripod and usually displaying an “out” configuration. Here, we demonstrate that solvents are able to control the “in” and “out” configurations of the CTV unit, creating a chiral molecular switch from (M/P)”in” to (P/M)”out” handedness. The full characterization of the “in” and “out” configurations and of the chirality switch were made possible by combining NMR, HPLC, ECD, DFT and molecular dynamics. Interestingly, bulky aromatic solvents such as 2‐t‐butylphenol favor the “in” configuration while polar aprotic solvents such as acetone favor the “out” configuration. This chiral switch was found to be fully reversible allowing the system to oscillate between two different M and P configurations several times upon the action of solvents stimuli.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Toldo2024,

title = {Recommendations for Velocity Adjustment in Surface Hopping},

author = {Josene M. Toldo and Rafael S. Mattos and Max Pinheiro and Saikat Mukherjee and Mario Barbatti},

doi = {10.1021/acs.jctc.3c01159},

issn = {1549-9626},

year  = {2024},

date = {2024-01-23},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {2},

pages = {614--624},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pieri2024,

title = {Modeling pH-Dependent Biomolecular Photochemistry},

author = {Elisa Pieri and Oliver Weingart and Miquel Huix-Rotllant and Vincent Ledentu and Marco Garavelli and Nicolas Ferré},

doi = {10.1021/acs.jctc.3c00980},

issn = {1549-9626},

year  = {2024},

date = {2024-01-23},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {2},

pages = {842--855},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Puthumana2024,

title = {Assessment of coupled bilayer–cytoskeleton modelling strategy for red blood cell dynamics in flow},

author = {V. Puthumana and P.G. Chen and M. Leonetti and R. Lasserre and M. Jaeger},

doi = {10.1017/jfm.2023.1092},

issn = {1469-7645},

year  = {2024},

date = {2024-01-22},

journal = {J. Fluid Mech.},

volume = {979},

publisher = {Cambridge University Press (CUP)},

abstract = {The red blood cell (RBC) membrane is composed of a lipid bilayer and a cytoskeleton interconnected by protein junction complexes, allowing for potential sliding between the lipid bilayer and the cytoskeleton. Despite this biological reality, it is most often modelled as a single-layer model, a hyperelastic capsule or a fluid vesicle. Another approach involves incorporating the membrane's composite structure using double layers, where one layer represents the lipid bilayer and the other represents the cytoskeleton. In this paper, we computationally assess the various modelling strategies by analysing RBC behaviour in extensional flow and four distinct regimes that simulate RBC dynamics in shear flow. The proposed double-layer strategies, such as the vesicle–capsule and capsule–capsule models, account for the fluidity and surface incompressibility of the lipid bilayer in different ways. Our findings demonstrate that introducing sliding between the layers offers the cytoskeleton a considerable degree of freedom to alleviate its elastic stresses, resulting in a significant increase in RBC elongation. Surprisingly, our study reveals that the membrane modelling strategy for RBCs holds greater importance than the choice of the cytoskeleton's reference shape. These results highlight the inadequacy of considering mechanical properties alone and emphasise the need for careful integration of these properties. Furthermore, our findings fortuitously uncover a novel indicator for determining the appropriate stress-free shape of the cytoskeleton.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Alías-Rodríguez2023,

title = {Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory},

author = {Marc Alías-Rodríguez and Simone Bonfrate and Woojin Park and Nicolas Ferré and Cheol Ho Choi and Miquel Huix-Rotllant},

doi = {10.1021/acs.jpca.3c05070},

issn = {1520-5215},

year  = {2023},

date = {2023-12-14},

journal = {J. Phys. Chem. A},

volume = {127},

number = {49},

pages = {10382--10392},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cárdenas2023,

title = {Automatic Rhodopsin Modeling with Multiple Protonation Microstates},

author = {Gustavo Cárdenas and Vincent Ledentu and Miquel Huix-Rotllant and Massimo Olivucci and Nicolas Ferré},

doi = {10.1021/acs.jpca.3c05413},

issn = {1520-5215},

year  = {2023},

date = {2023-11-09},

journal = {J. Phys. Chem. A},

volume = {127},

number = {44},

pages = {9365--9380},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LiManni2023,

title = {The OpenMolcas \textit{Web}: A Community-Driven Approach to Advancing Computational Chemistry},

author = {Giovanni Li Manni and Ignacio Fdez. Galván and Ali Alavi and Flavia Aleotti and Francesco Aquilante and Jochen Autschbach and Davide Avagliano and Alberto Baiardi and Jie J. Bao and Stefano Battaglia and Letitia Birnoschi and Alejandro Blanco-González and Sergey I. Bokarev and Ria Broer and Roberto Cacciari and Paul B. Calio and Rebecca K. Carlson and Rafael Carvalho Couto and Luis Cerdán and Liviu F. Chibotaru and Nicholas F. Chilton and Jonathan Richard Church and Irene Conti and Sonia Coriani and Juliana Cuéllar-Zuquin and Razan E. Daoud and Nike Dattani and Piero Decleva and Coen de Graaf and Mickaël G. Delcey and Luca De Vico and Werner Dobrautz and Sijia S. Dong and Rulin Feng and Nicolas Ferré and Michael Filatov(Gulak) and Laura Gagliardi and Marco Garavelli and Leticia González and Yafu Guan and Meiyuan Guo and Matthew R. Hennefarth and Matthew R. Hermes and Chad E. Hoyer and Miquel Huix-Rotllant and Vishal Kumar Jaiswal and Andy Kaiser and Danil S. Kaliakin and Marjan Khamesian and Daniel S. King and Vladislav Kochetov and Marek Krośnicki and Arpit Arun Kumaar and Ernst D. Larsson and Susi Lehtola and Marie-Bernadette Lepetit and Hans Lischka and Pablo López Ríos and Marcus Lundberg and Dongxia Ma and Sebastian Mai and Philipp Marquetand and Isabella C. D. Merritt and Francesco Montorsi and Maximilian Mörchen and Artur Nenov and Vu Ha Anh Nguyen and Yoshio Nishimoto and Meagan S. Oakley and Massimo Olivucci and Markus Oppel and Daniele Padula and Riddhish Pandharkar and Quan Manh Phung and Felix Plasser and Gerardo Raggi and Elisa Rebolini and Markus Reiher and Ivan Rivalta and Daniel Roca-Sanjuán and Thies Romig and Arta Anushirwan Safari and Aitor Sánchez-Mansilla and Andrew M. Sand and Igor Schapiro and Thais R. Scott and Javier Segarra-Martí and Francesco Segatta and Dumitru-Claudiu Sergentu and Prachi Sharma and Ron Shepard and Yinan Shu and Jakob K. Staab and Tjerk P. Straatsma and Lasse Kragh Sørensen and Bruno Nunes Cabral Tenorio and Donald G. Truhlar and Liviu Ungur and Morgane Vacher and Valera Veryazov and Torben Arne Voß and Oskar Weser and Dihua Wu and Xuchun Yang and David Yarkony and Chen Zhou and J. Patrick Zobel and Roland Lindh},

doi = {10.1021/acs.jctc.3c00182},

issn = {1549-9626},

year  = {2023},

date = {2023-10-24},

journal = {J. Chem. Theory Comput.},

volume = {19},

number = {20},

pages = {6933--6991},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{He2023,

title = {Internal shear layers in librating spherical shells: the case of attractors},

author = {Jiyang He and Benjamin Favier and Michel Rieutord and Stéphane Le Dizès},

doi = {10.1017/jfm.2023.761},

issn = {1469-7645},

year  = {2023},

date = {2023-10-23},

journal = {J. Fluid Mech.},

volume = {974},

publisher = {Cambridge University Press (CUP)},

abstract = {Following our previous work on periodic ray paths (He et al., J. Fluid Mech., vol. 939, 2022, A3), we study asymptotically and numerically the structure of internal shear layers for very small Ekman numbers in a three-dimensional spherical shell and in a two-dimensional cylindrical annulus when the rays converge towards an attractor. We first show that the asymptotic solution obtained by propagating the self-similar solution generated at the critical latitude on the librating inner core describes the main features of the numerical solution. The internal shear layer structure and the scaling for its width and velocity amplitude in 

	      

		

		$E^{1/3}$

	      

	     and 

	      

		

		$E^{1/12}$

	      

	    , respectively, are recovered. The amplitude of the asymptotic solution is shown to decrease to 

	      

		

		$E^{1/6}$

	      

	     when it reaches the attractor, as is also observed numerically. However, some discrepancies are observed close to the particular attractors along which the phase of the wave beam remains constant. Another asymptotic solution close to those attractors is then constructed using the model of Ogilvie (J. Fluid Mech., vol. 543, 2005, pp. 19–44). The solution obtained for the velocity has an 

	      

		

		$O(E^{1/6})$

	      

	     amplitude, but a self-similar structure different from the critical-latitude solution. It also depends on the Ekman pumping at the contact points of the attractor with the boundaries. We demonstrate that it reproduces correctly the numerical solution. Surprisingly, the numerical solution close to an attractor with phase shift (that is, an attractor touching the axis in three or two dimensions with a symmetric forcing) is also found to be 

	      

		

		$O(E^{1/6})$

	      

	    , but its amplitude is much weaker. However, its asymptotic structure remains a mystery.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mansour2023,

title = {Temperature effects on the internal conversion of excited adenine and adenosine},

author = {Ritam Mansour and Josene M. Toldo and Saikat Mukherjee and Max Pinheiro and Mario Barbatti},

doi = {10.1039/d3cp03234e},

issn = {1463-9084},

year  = {2023},

date = {2023-10-18},

journal = {Phys. Chem. Chem. Phys.},

volume = {25},

number = {40},

pages = {27083--27093},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {Temperature has a strikingly different impact on adenine and adenosine photodynamics. Surface hopping reveals the reason underlying it.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sun2023,

title = {Asymmetric Allenylation of Alkynes mediated by Chiral Organoselenated Reagents under Oxidative Conditions},

author = {Rongyu Sun and Emilie Viaud and Rajesh Nomula and Jean‐Valère Naubron and Nicolas Daugey and Thierry Buffeteau and Frédéric Castet and Patrick Y. Toullec and Stéphane Quideau and Philippe A. Peixoto},

doi = {10.1002/anie.202310436},

issn = {1521-3773},

year  = {2023},

date = {2023-10-16},

journal = {Angew Chem Int Ed},

volume = {62},

number = {42},

publisher = {Wiley},

abstract = {AbstractThe reactivity of novel chiral lactamide‐substituted diselenide‐based reagents under oxidative conditions was exploited to develop a metal‐free method for the preparation of enantioenriched allenylamides from simple alkynes in good yields, and with enantiomeric excesses up to 99 %. The key of the success in this method is attributed to the hydrogen‐bonded lactamide appendages that ensure configurational stability of chiral vinyl selenoxide intermediates for an optimal enantiotopic β‐syn‐elimination step.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dalton2023,

title = {Understanding the Impact of Symmetrical Substitution on the Photodynamics of Sinapate Esters Using Gas-Phase Ultrafast Spectroscopy},

author = {Jack Dalton and Josene M. Toldo and Florent Allais and Mario Barbatti and Vasilios G. Stavros},

doi = {10.1021/acs.jpclett.3c02134},

issn = {1948-7185},

year  = {2023},

date = {2023-10-05},

journal = {J. Phys. Chem. Lett.},

volume = {14},

number = {39},

pages = {8771--8779},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Alías-Rodríguez2023b,

title = {Ultrafast Spin Crossover Photochemical Mechanism in [Fe^{II}(2,2′-bipyridine)_{3}]^{2+}] Revealed by Quantum Dynamics},

author = {Marc Alías-Rodríguez and Swarnendu Bhattacharyya and Miquel Huix-Rotllant},

doi = {10.1021/acs.jpclett.3c02201},

issn = {1948-7185},

year  = {2023},

date = {2023-09-28},

journal = {J. Phys. Chem. Lett.},

volume = {14},

number = {38},

pages = {8571--8576},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doCasal2023,

title = {Classification of doubly excited molecular electronic states},

author = {Mariana T. do Casal and Josene M. Toldo and Mario Barbatti and Felix Plasser},

doi = {10.1039/d2sc06990c},

issn = {2041-6539},

year  = {2023},

date = {2023-04-12},

journal = {Chem. Sci.},

volume = {14},

number = {15},

pages = {4012--4026},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {A rigorous classification scheme for doubly excited states is proposed and the different possible types are exemplified in various molecules.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bonfrate2023,

title = {An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators},

author = {Simone Bonfrate and Nicolas Ferré and Miquel Huix-Rotllant},

doi = {10.1063/5.0133646},

issn = {1089-7690},

year  = {2023},

date = {2023-01-14},

volume = {158},

number = {2},

publisher = {AIP Publishing},

abstract = {Hybrid quantum mechanics/molecular mechanics (QM/MM) models are successful at describing the properties and reactivity of biological macromolecules. Combining ab initio QM/MM methods and periodic boundary conditions (PBC) is currently the optimal approach for modeling chemical processes in an infinite environment, but frequently, these models are too time-consuming for general applicability to biological systems in a solution. Here, we define a simple and efficient electrostatic embedding QM/MM model in PBC, combining the benefits of electrostatic potential fitted atomic charges and particle-mesh Ewald sums, which can efficiently treat systems of an arbitrary size at a reasonable computational cost. To illustrate this, we apply our scheme to extract the lowest singlet excitation energies from a model for Arabidopsis thaliana cryptochrome 1 containing circa 93 000 atoms, accurately reproducing the experimental absorption maximum.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{David2022,

title = {Consistent Evaluation of Magnetic Exchange Couplings in Multicenter Compounds in KS-DFT: The Recomposition Method},

author = {Grégoire David and Nicolas Ferré and Boris Le Guennic},

doi = {10.1021/acs.jctc.2c01022},

issn = {1549-9626},

year  = {2023},

date = {2023-01-10},

journal = {J. Chem. Theory Comput.},

volume = {19},

number = {1},

pages = {157--173},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huix-Rotllant2022,

title = {Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT},

author = {Miquel Huix-Rotllant and Karno Schwinn and Vladimir Pomogaev and Maryam Farmani and Nicolas Ferré and Seunghoon Lee and Cheol Ho Choi},

doi = {10.1021/acs.jctc.2c01010},

issn = {1549-9626},

year  = {2023},

date = {2023-01-10},

journal = {J. Chem. Theory Comput.},

volume = {19},

number = {1},

pages = {147--156},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vanKan2022,

title = {Spontaneous suppression of inverse energy cascade in instability-driven 2-D turbulence},

author = {Adrian van Kan and Benjamin Favier and Keith Julien and Edgar Knobloch},

doi = {10.1017/jfm.2022.935},

issn = {1469-7645},

year  = {2022},

date = {2022-12-01},

journal = {J. Fluid Mech.},

volume = {952},

publisher = {Cambridge University Press (CUP)},

abstract = {Instabilities of fluid flows often generate turbulence. Using extensive direct numerical simulations, we study two-dimensional turbulence driven by a wavenumber-localised instability superposed on stochastic forcing, in contrast to previous studies of state-independent forcing. As the contribution of the instability forcing, measured by a parameter 

	      

		

		$gamma$

	      

	    , increases, the system undergoes two transitions. For 

	      

		

		$gamma$

	      

	     below a first threshold, a regular large-scale vortex condensate forms. Above this threshold, shielded vortices (SVs) emerge within the condensate. At a second, larger value of 

	      

		

		$gamma$

	      

	    , the condensate breaks down, and a gas of weakly interacting vortices with broken symmetry spontaneously emerges, characterised by preponderance of vortices of one sign only and suppressed inverse energy cascade. The latter transition is shown to depend on the damping mechanism. The number density of SVs in the broken symmetry state slowly increases via a random nucleation process. Bistability is observed between the condensate and mixed SV-condensate states. Our findings provide new evidence for a strong dependence of two-dimensional turbulence phenomenology on the forcing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Braun2022,

title = {Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium between excited states},

author = {Gabriel Braun and Itamar Borges and Adélia J. A. Aquino and Hans Lischka and Felix Plasser and Silmar A. do Monte and Elizete Ventura and Saikat Mukherjee and Mario Barbatti},

doi = {10.1063/5.0113908},

issn = {1089-7690},

year  = {2022},

date = {2022-10-21},

volume = {157},

number = {15},

publisher = {AIP Publishing},

abstract = {Pyrene fluorescence after a high-energy electronic excitation exhibits a prominent band shoulder not present after excitation at low energies. The standard assignment of this shoulder as a non-Kasha emission from the second-excited state (S2) has been recently questioned. To elucidate this issue, we simulated the fluorescence of pyrene using two different theoretical approaches based on vertical convolution and nonadiabatic dynamics with nuclear ensembles. To conduct the necessary nonadiabatic dynamics simulations with high-lying electronic states and deal with fluorescence timescales of about 100 ns of this large molecule, we developed new computational protocols. The results from both approaches confirm that the band shoulder is, in fact, due to S2 emission. We show that the non-Kasha behavior is a dynamic-equilibrium effect not caused by a metastable S2 minimum. However, it requires considerable vibrational energy, which can only be achieved in collisionless regimes after transitions into highly excited states. This strict condition explains why the S2 emission was not observed in some experiments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doCasal2022,

title = {Using diketopyrrolopyrroles to stabilize double excitation and control internal conversion},

author = {Mariana T. do Casal and Josene M. Toldo and Felix Plasser and Mario Barbatti},

doi = {10.1039/d2cp03533b},

issn = {1463-9084},

year  = {2022},

date = {2022-10-05},

journal = {Phys. Chem. Chem. Phys.},

volume = {24},

number = {38},

pages = {23279--23288},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {Diketopyrrolopyrrole (DPP) units can be used to stabilize the doubly excited state (2Ag) and control internal conversion by increasing the number of π-electrons.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kadoch2022,

title = {Lagrangian conditional statistics and flow topology in edge plasma turbulence},

author = {Benjamin Kadoch and Diego del-Castillo-Negrete and Wouter J. T. Bos and Kai Schneider},

doi = {10.1063/5.0098501},

issn = {1089-7674},

year  = {2022},

date = {2022-10-01},

volume = {29},

number = {10},

publisher = {AIP Publishing},

abstract = {Lagrangian statistics and particle transport in edge plasma turbulence are investigated using the Hasegawa–Wakatani model and its modified version. The latter shows the emergence of pronounced zonal flows. Different values of the adiabaticity parameter are considered. The main goal is to characterize the role of coherent structures, i.e., vortices and zonal flows, and their impact on the Lagrangian statistics of particles. Computationally intensive long time simulations following ensembles of test particles over hundreds of eddy turnover times are considered in statistically stationary turbulent flows. The flow topology is characterized using the Lagrangian Okubo–Weiss criterion in order to split the flow into topologically different domains. In elliptic and hyperbolic regions, the probability density functions (PDFs) of the residence time have self-similar algebraic decaying tails. However, in the intermediate regions, the PDFs exhibit exponentially decaying tails. Topologically conditioned PDFs of the Lagrangian velocity, and acceleration and density fluctuations are likewise computed. The differences between the classical Hasegawa–Wakatani system and its modified version are assessed, and the role of zonal flows is highlighted. The density flux spectrum, which characterizes the contributions of different length scales, is studied, and its inertial scaling is found to be in agreement with predictions based on dimensional arguments. Analyzing the angular change of particle tracers at different time scales, corresponding to coarse grained curvature, completes the study, and these multiscale geometric statistics quantify the directional properties of the particle motion in different flow regimes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chaussy2022,

title = {Accurate computed singlet–triplet energy differences for cobalt systems: implication for two-state reactivity},

author = {Léo Chaussy and Denis Hagebaum-Reignier and Stéphane Humbel and Paola Nava},

doi = {10.1039/d2cp03291k},

issn = {1463-9084},

year  = {2022},

date = {2022-09-21},

journal = {Phys. Chem. Chem. Phys.},

volume = {24},

number = {36},

pages = {21841--21852},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {Accurate singlet–triplet energy differences for cobalt and rhodium complexes are obtained at high computational level (MRCISD, CASPT2, CCSD(T), DFT). Our results have an impact on the mechanism of cobalt cycloaddition reactions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cai2022,

title = {Application of immersed boundary based turbulence wall modeling to the Ahmed body aerodynamics},

author = {Shang-Gui Cai and Sajad Mozaffari and Jérôme Jacob and Pierre Sagaut},

doi = {10.1063/5.0098232},

issn = {1089-7666},

year  = {2022},

date = {2022-09-01},

volume = {34},

number = {9},

publisher = {AIP Publishing},

abstract = {This paper applies a recently developed immersed boundary-turbulence wall modeling approach to turbulent flows over a generic car geometry, known as the Ahmed body, under massive flow separation within a lattice Boltzmann solver. Although the immersed boundary method combined with hierarchical Cartesian grid offers high flexibility in automatic grid generation around complex geometries, the near-wall solution is significantly deteriorated compared to the body-fitted simulation, especially when coupled to wall models for turbulent flows at high Reynolds number. Enhanced wall treatments have been proposed in the literature and validated for attached flow configurations. In this work, the Ahmed body with a slant surface of angle 35° is considered where the flow separates massively over the slant surface and the vertical base. The large eddy simulation is performed with a Reynolds stress constraint near-wall. The eddy viscosity is computed dynamically by taking into account the actually resolved Reynolds stresses. It approaches the mixing length eddy viscosity in attached boundary layers and returns to the subgrid eddy viscosity in detached boundary layers. An explicit equilibrium wall model has also been proposed to accelerate the calculation. Comparison with the no-slip boundary condition on the separated surfaces shows that the near-wall treatments with the equilibrium wall model operate reasonably well on both attached and detached boundary layers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Polak2022,

title = {Probing the electronic structure and photophysics of thiophene–diketopyrrolopyrrole derivatives in solution},

author = {Daniel W. Polak and Mariana T. do Casal and Josene M. Toldo and Xiantao Hu and Giordano Amoruso and Olivia Pomeranc and Martin Heeney and Mario Barbatti and Michael N. R. Ashfold and Thomas A. A. Oliver},

doi = {10.1039/d2cp03238d},

issn = {1463-9084},

year  = {2022},

date = {2022-08-31},

journal = {Phys. Chem. Chem. Phys.},

volume = {24},

number = {34},

pages = {20138--20151},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {The interplay of two excited electronic states dictates the ultrafast dynamics and functionality of thiophene-diketopyrrolopyrrole derivatives.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Polak2022b,

title = {Probing the electronic structure and photophysics of thiophene–diketopyrrolopyrrole derivatives in solution},

author = {Daniel W. Polak and Mariana T. do Casal and Josene M. Toldo and Xiantao Hu and Giordano Amoruso and Olivia Pomeranc and Martin Heeney and Mario Barbatti and Michael N. R. Ashfold and Thomas A. A. Oliver},

doi = {10.1039/d2cp03238d},

issn = {1463-9084},

year  = {2022},

date = {2022-08-31},

journal = {Phys. Chem. Chem. Phys.},

volume = {24},

number = {34},

pages = {20138--20151},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {The interplay of two excited electronic states dictates the ultrafast dynamics and functionality of thiophene-diketopyrrolopyrrole derivatives.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Couston2022,

title = {Competition between Rayleigh–Bénard and horizontal convection},

author = {Louis-Alexandre Couston and Joseph Nandaha and Benjamin Favier},

doi = {10.1017/jfm.2022.613},

issn = {1469-7645},

year  = {2022},

date = {2022-08-22},

journal = {J. Fluid Mech.},

volume = {947},

publisher = {Cambridge University Press (CUP)},

abstract = {We investigate the dynamics of a fluid layer subject to a bottom heat flux and a top monotonically increasing temperature profile driving horizontal convection (HC). We use direct numerical simulations and consider a large range of flux-based Rayleigh numbers 

	      

		

		$10^6 leq Ra_F leq 10^9$

	      

	     and imposed top horizontal to bottom vertical heat flux ratios 

	      

		

		$0 leq varLambda leq 1$

	      

	    . The fluid domain is a closed two-dimensional box with aspect ratio 

	      

		

		$4leq varGamma leq 16$

	      

	     and we consider no-slip boundaries and adiabatic side walls. We demonstrate a regime transition from Rayleigh–Bénard (RB) convection to HC at 

	      

		

		$varLambda approx 10^{-2}$

	      

	    , which is independent of 

	      

		

		$Ra_F$

	      

	     and 

	      

		

		$varGamma$

	      

	    . At small 

	      

		

		$varLambda$

	      

	    , the flow is organised in multiple overturning cells with approximately unit aspect ratio, whereas at large 

	      

		

		$varLambda$

	      

	     a single cell is obtained. The RB-relevant Nusselt number scaling with 

	      

		

		$Ra_F$

	      

	     and the HC-relevant Nusselt number scaling with the horizontal Rayleigh number 

	      

		

		$Ra_L=Ra_FvarLambda varGamma ^4$

	      

	     are in good agreement with previous results from classical RB convection and HC studies in the limit 

	      

		

		$varLambda ll 10^{-2}$

	      

	     and 

	      

		

		$varLambda gg 10^{-2}$

	      

	    , respectively. We demonstrate that the system is multi-stable near the transition 

	      

		

		$varLambda approx 10^{-2}$

	      

	    , i.e. the exact number of cells not only depends on 

	      

		

		$varLambda$

	      

	     but also on the system's history. Our results suggest that subglacial lakes, which motivated this study, are likely to be dominated by RB convection, unless the slope of the ice–water interface, which controls the horizontal temperature gradient via the pressure-dependence of the freezing point, is greater than unity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mukherjee2022,

title = {A Hessian-Free Method to Prevent Zero-Point Energy Leakage in Classical Trajectories},

author = {Saikat Mukherjee and Mario Barbatti},

doi = {10.1021/acs.jctc.2c00216},

issn = {1549-9626},

year  = {2022},

date = {2022-07-12},

journal = {J. Chem. Theory Comput.},

volume = {18},

number = {7},

pages = {4109--4116},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mansour2022,

title = {Pre-Dewar structure modulates protonated azaindole photodynamics},

author = {Ritam Mansour and Saikat Mukherjee and Max Pinheiro and Jennifer A. Noble and Christophe Jouvet and Mario Barbatti},

doi = {10.1039/d2cp01056a},

issn = {1463-9084},

year  = {2022},

date = {2022-05-25},

journal = {Phys. Chem. Chem. Phys.},

volume = {24},

number = {20},

pages = {12346--12353},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {Nonadiabatic surface hopping simulations demonstrate that the lifetime of the S3 state of protonated 7-azaindole is much longer than that of protonated 6-azaindole due to a puckered pre-Dewar structure in the S3 minimum of the 7-isomer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bonnet2022,

title = {Morphology of dark matter haloes beyond triaxiality},

author = {G Bonnet and E Nezri and K Kraljic and C Schimd},

doi = {10.1093/mnras/stac1222},

issn = {1365-2966},

year  = {2022},

date = {2022-05-23},

volume = {513},

number = {4},

pages = {4929--4944},

publisher = {Oxford University Press (OUP)},

abstract = {ABSTRACT

               The morphology of haloes inform about both cosmological and galaxy formation models. We use the Minkowski Functionals (MFs) to characterize the actual morphology of haloes, only partially captured by smooth density profile, going beyond the spherical or ellipsoidal symmetry. We employ semi-analytical haloes with NFW and αβγ-profile and spherical or ellipsoidal shape to obtain a clear interpretation of MFs as function of inner and outer slope, concentration and sphericity parameters. We use the same models to mimic the density profile of N-body haloes, showing that their MFs clearly differ as sensitive to internal substructures. This highlights the benefit of MFs at the halo scales as promising statistics to improve the spatial modelling of dark matter, crucial for future lensing, Sunyaev–Zel’dovich, and X-ray mass maps as well as dark matter detection based on high-accuracy data.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Taha2022,

title = {Lattice-Boltzmann modeling of buoyancy-driven turbulent flows},

author = {M. Taha and S. Zhao and A. Lamorlette and J. L. Consalvi and P. Boivin},

doi = {10.1063/5.0088409},

issn = {1089-7666},

year  = {2022},

date = {2022-05-01},

volume = {34},

number = {5},

publisher = {AIP Publishing},

abstract = {The pressure-based hybrid lattice-Boltzmann method presented by Farag et al. [“A pressure-based regularized lattice-Boltzmann method for the simulation of compressible flows,” Phys. Fluids 32, 066106 (2020)] is assessed for the simulation of buoyancy driven flows. The model is first validated on Rayleigh–Benard and Rayleigh–Taylor two-dimensional cases. A large-eddy simulation of a turbulent forced plume is then carried out, and results are validated against experiments. Good overall agreement is obtained, both for mean and fluctuation quantities, as well as global entrainment. The self-similarity characteristic of the plume in the far-field is also recovered.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bufferand2022,

title = {Implementation of multi-component Zhdanov closure in SOLEDGE3X},

author = {H Bufferand and J Balbin and S Baschetti and J Bucalossi and G Ciraolo and Ph Ghendrih and R Mao and N Rivals and P Tamain and H Yang and G Giorgiani and F Schwander and M Scotto d’Abusco and E Serre and J Denis and Y Marandet and M Raghunathan and P Innocente and D Galassi and },

doi = {10.1088/1361-6587/ac4fac},

issn = {1361-6587},

year  = {2022},

date = {2022-05-01},

journal = {Plasma Phys. Control. Fusion},

volume = {64},

number = {5},

publisher = {IOP Publishing},

abstract = {Abstract

               The multi-component fluid closure derived by Zhdanov (2002 Transport Processes in Multicomponent Plasma (London: Taylor and Francis)) is implemented in the fluid code SOLEDGE3X-EIRENE to deal with arbitrary edge plasma composition. The closure assumes no distinction between species such as light versus heavy species separation. The work of Zhdanov is rewritten in a matricial form in order to clearly link friction forces and heat fluxes to the different species velocities and temperature gradients.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wissocq2022,

title = {Restoring the conservativity of characteristic-based segregated models: Application to the hybrid lattice Boltzmann method},

author = {G. Wissocq and T. Coratger and G. Farag and S. Zhao and P. Boivin and P. Sagaut},

doi = {10.1063/5.0083377},

issn = {1089-7666},

year  = {2022},

date = {2022-04-01},

volume = {34},

number = {4},

publisher = {AIP Publishing},

abstract = {A general methodology is introduced to build conservative numerical models for fluid simulations based on segregated schemes, where mass, momentum, and energy equations are solved by different methods. It is especially designed here for developing new numerical discretizations of the total energy equation and adapted to a thermal coupling with the lattice Boltzmann method (LBM). The proposed methodology is based on a linear equivalence with standard discretizations of the entropy equation, which, as a characteristic variable of the Euler system, allows efficiently decoupling the energy equation with the LBM. To this extent, any LBM scheme is equivalently written under a finite-volume formulation involving fluxes, which are further included in the total energy equation as numerical corrections. The viscous heat production is implicitly considered thanks to the knowledge of the LBM momentum flux. Three models are subsequently derived: a first-order upwind, a Lax–Wendroff, and a third-order Godunov-type schemes. They are assessed on standard academic test cases: a Couette flow, entropy spot and vortex convections, a Sod shock tube, several two-dimensional Riemann problems, and a shock–vortex interaction. Three key features are then exhibited: (1) the models are conservative by construction, recovering correct jump relations across shock waves; (2) the stability and accuracy of entropy modes can be explicitly controlled; and (3) the low dissipation of the LBM for isentropic phenomena is preserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hodille2021,

title = {Modelling of hydrogen isotopes trapping, diffusion and permeation in divertor monoblocks under ITER-like conditions},

author = {E.A. Hodille and R. Delaporte-Mathurin and J. Denis and M. Pecovnik and E. Bernard and Y. Ferro and R. Sakamoto and Y. Charles and J. Mougenot and A. De Backer and C.S. Becquart and S. Markelj and C. Grisolia},

doi = {10.1088/1741-4326/ac2abc},

issn = {1741-4326},

year  = {2021},

date = {2021-12-01},

journal = {Nucl. Fusion},

volume = {61},

number = {12},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Abiola2021,

title = {Towards developing novel and sustainable molecular light-to-heat converters},

author = {Temitope T. Abiola and Benjamin Rioux and Josene M. Toldo and Jimmy Alarcan and Jack M. Woolley and Matthew A. P. Turner and Daniel J. L. Coxon and Mariana Telles do Casal and Cédric Peyrot and Matthieu M. Mention and Wybren J. Buma and Michael N. R. Ashfold and Albert Braeuning and Mario Barbatti and Vasilios G. Stavros and Florent Allais},

doi = {10.1039/d1sc05077j},

issn = {2041-6539},

year  = {2021},

date = {2021-12-01},

journal = {Chem. Sci.},

volume = {12},

number = {46},

pages = {15239--15252},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {The synthesis and photophysical properties of phenolic barbiturics are reported. These molecules convert absorbed ultraviolet light to heat with high fidelity and may be suitable for inclusion in foliar sprays to boost crop protection and production.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Coratger2021,

title = {Large-eddy lattice-Boltzmann modeling of transonic flows},

author = {T. Coratger and G. Farag and S. Zhao and P. Boivin and P. Sagaut},

doi = {10.1063/5.0064944},

issn = {1089-7666},

year  = {2021},

date = {2021-11-01},

volume = {33},

number = {11},

publisher = {AIP Publishing},

abstract = {A D3Q19 hybrid recursive regularized pressure based lattice-Boltzmann method (HRR-P LBM) is assessed for the simulation of complex transonic flows. Mass and momentum conservation equations are resolved through a classical LBM solver coupled with a finite volume resolution of entropy equation for a complete compressible solver preserving stability, accuracy, and computational costs. An efficient treatment for wall and open boundaries is coupled with a grid refinement technique and extended to the HRR-P LBM in the scope of compressible aerodynamics. A Vreman subgrid turbulence model and an improved coupling of immersed boundary method with turbulence wall model on Cartesian grid accounts for unresolved scales by large-eddy simulation. The validity of the present method for transonic applications is investigated through various test cases with increasing complexity starting from an inviscid flow over a 10% bump and ending with a turbulent flow over a ONERA M6 three-dimensional wing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2021,

title = {Large temperature difference heat dominated flow simulations using a pressure-based lattice Boltzmann method with mass correction},

author = {Guanxiong Wang and Lincheng Xu and Eric Serre and Pierre Sagaut},

doi = {10.1063/5.0073178},

issn = {1089-7666},

year  = {2021},

date = {2021-11-01},

volume = {33},

number = {11},

publisher = {AIP Publishing},

abstract = {This paper addresses simulation of heat dominated compressible flows in a closed cavity using a pressure-based lattice Boltzmann (LB) method, in which thermal effects are modeled by applying a pressure-featured zero-order moment of distribution functions. A focus is made on the conservation of mass at boundary nodes, which is a challenging issue that significantly complicated by the density-decoupled zero-order moment here. The mass leakage at boundary nodes is mathematically quantified, which enables an efficient local mass correction scheme. The performance of this solver is assessed by simulating buoyancy-driven flows in a closed deferentially heated cavity with large temperature differences (non-Boussinesq) at Rayleigh numbers ranging from 103 to 107. Simulations show that mass leakage at solid walls in such configurations is a critical issue to obtain reliable solutions, and it eventually leads to simulations overflow when the cavity is inclined. The proposed mass correction scheme is, however, shown to be effective to control the mass leakage and get accurate solutions. Thus, associated with the proposed mass conservation scheme, the pressure-based LB method becomes reliable to study natural convection dominated flows at large temperature differences in closed geometries with mesh aligned boundaries or not.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Truong2021b,

title = {An experimental data-driven mass-spring model of flexible \textit{Calliphora} wings},

author = {Hung Truong and Thomas Engels and Henja Wehmann and Dmitry Kolomenskiy and Fritz-Olaf Lehmann and Kai Schneider},

doi = {10.1088/1748-3190/ac2f56},

issn = {1748-3190},

year  = {2021},

date = {2021-10-13},

journal = {Bioinspir. Biomim.},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Truong2021,

title = {An experimental data-driven mass-spring model of flexible \textit{Calliphora} wings},

author = {Hung Truong and Thomas Engels and Henja Wehmann and Dmitry Kolomenskiy and Fritz-Olaf Lehmann and Kai Schneider},

doi = {10.1088/1748-3190/ac2f56},

issn = {1748-3190},

year  = {2021},

date = {2021-10-13},

journal = {Bioinspir. Biomim.},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bouffard2021,

title = {Internal gravity waves in a stratified layer atop a convecting liquid core in a non-rotating spherical shell},

author = {M Bouffard and B Favier and D Lecoanet and M Le Bars},

doi = {10.1093/gji/ggab343},

issn = {1365-246X},

year  = {2021},

date = {2021-09-12},

volume = {228},

number = {1},

pages = {337--354},

publisher = {Oxford University Press (OUP)},

abstract = {SUMMARY

               Seismic and magnetic observations have suggested the presence of a stably stratified layer atop Earth’s core. Such a layer could affect the morphology of the geomagnetic field and the evolution of the core, but the precise impact of this layer depends largely on its internal dynamics. Among other physical phenomena, stratified layers host internal gravity waves (IGW), which can be excited by adjacent convective motions. Internal waves are known to play an important role on the large-scale dynamics of the Earth’s climate and on the long-term evolution of stars. Yet, they have received relatively little attention in the Earth’s outer core so far and deserve detailed investigations in this context. Here, we make a first step in that direction by running numerical simulations of IGW in a non-rotating spherical shell in which a stratified layer lies on top of a convective region. We use a nonlinear equation of state to produce self-consistently such a two-layer system. Both propagating waves and global modes coexist in the stratified layer. We characterize the spectral properties of these waves and find that energy is distributed across a wide range of frequencies and length scales, that depends on the Prandtl number. For the control parameters considered and in the absence of rotational and magnetic effects, the mean kinetic energy in the layer is about 0.1 per cent that of the convective region. IGW produce perturbations in the gravity field that may fall within the sensitivity limit of present-day instruments and could potentially be detected in available data. We finally provide a road map for future, more geophysically realistic, studies towards a more thorough understanding of the dynamics and impact of internal waves in a stratified layer atop Earth’s core.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bouffard2021b,

title = {Internal gravity waves in a stratified layer atop a convecting liquid core in a non-rotating spherical shell},

author = {M Bouffard and B Favier and D Lecoanet and M Le Bars},

doi = {10.1093/gji/ggab343},

issn = {1365-246X},

year  = {2021},

date = {2021-09-12},

volume = {228},

number = {1},

pages = {337--354},

publisher = {Oxford University Press (OUP)},

abstract = {SUMMARY

               Seismic and magnetic observations have suggested the presence of a stably stratified layer atop Earth’s core. Such a layer could affect the morphology of the geomagnetic field and the evolution of the core, but the precise impact of this layer depends largely on its internal dynamics. Among other physical phenomena, stratified layers host internal gravity waves (IGW), which can be excited by adjacent convective motions. Internal waves are known to play an important role on the large-scale dynamics of the Earth’s climate and on the long-term evolution of stars. Yet, they have received relatively little attention in the Earth’s outer core so far and deserve detailed investigations in this context. Here, we make a first step in that direction by running numerical simulations of IGW in a non-rotating spherical shell in which a stratified layer lies on top of a convective region. We use a nonlinear equation of state to produce self-consistently such a two-layer system. Both propagating waves and global modes coexist in the stratified layer. We characterize the spectral properties of these waves and find that energy is distributed across a wide range of frequencies and length scales, that depends on the Prandtl number. For the control parameters considered and in the absence of rotational and magnetic effects, the mean kinetic energy in the layer is about 0.1 per cent that of the convective region. IGW produce perturbations in the gravity field that may fall within the sensitivity limit of present-day instruments and could potentially be detected in available data. We finally provide a road map for future, more geophysically realistic, studies towards a more thorough understanding of the dynamics and impact of internal waves in a stratified layer atop Earth’s core.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gomes2021,

title = {Low-dimensional chaos in the single wave model for self-consistent wave–particle Hamiltonian},

author = {J. V. Gomes and M. C. de Sousa and R. L. Viana and I. L. Caldas and Y. Elskens},

doi = {10.1063/5.0040939},

issn = {1089-7682},

year  = {2021},

date = {2021-08-01},

volume = {31},

number = {8},

publisher = {AIP Publishing},

abstract = {We analyze nonlinear aspects of the self-consistent wave–particle interaction using Hamiltonian dynamics in the single wave model, where the wave is modified due to the particle dynamics. This interaction plays an important role in the emergence of plasma instabilities and turbulence. The simplest case, where one particle (N=1) is coupled with one wave (M=1), is completely integrable, and the nonlinear effects reduce to the wave potential pulsating while the particle either remains trapped or circulates forever. On increasing the number of particles (N=2, M=1), integrability is lost and chaos develops. Our analyses identify the two standard ways for chaos to appear and grow (the homoclinic tangle born from a separatrix, and the resonance overlap near an elliptic fixed point). Moreover, a strong form of chaos occurs when the energy is high enough for the wave amplitude to vanish occasionally.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Das2021,

title = {Effect of pulse width on the dynamics of a deflated vesicle in unipolar and bipolar pulsed electric fields},

author = {Sudip Das and Marc Jaeger and Marc Leonetti and Rochish M. Thaokar and Paul G. Chen},

doi = {10.1063/5.0057168},

issn = {1089-7666},

year  = {2021},

date = {2021-08-01},

volume = {33},

number = {8},

publisher = {AIP Publishing},

abstract = {Giant unilamellar vesicles subjected to pulsed direct-current (pulsed-DC) fields are promising biomimetic systems to investigate the electroporation of cells. In strong electric fields, vesicles undergo significant deformation, which strongly alters the transmembrane potential, and consequently the electroporation. Previous theoretical studies investigated the electrodeformation of vesicles in DC fields (which are not pulsed). In this work, we computationally investigate the deformation of a deflated vesicle under unipolar, bipolar, and two-step unipolar pulses and show the sensitive dependence of intermediate shapes on the type of pulse and pulse width. Starting with the stress-free initial shape of a deflated vesicle, which is similar to a prolate spheroid, the analysis is presented for the cases with higher and lower conductivities of the inner fluid medium relative to the outer fluid medium. For the ratio of inner to outer fluid conductivity, σr = 10, the shape always remains prolate, including when the field is turned off. For σr=0.1, several complex dynamics are observed, such as the prolate-to-oblate (PO), prolate-to-oblate-to-prolate (POP) shape transitions in time depending upon the strength of the field and the pulse properties. In this case, on turning off the field, a metastable oblate equilibrium shape is seen, which seems to be a characteristic of a deflated vesicle leading to POPO transitions. When a two-step unipolar pulse (a combination of a strong and a weak subpulse) is applied, a vesicle can reach an oblate or a prolate final shape depending upon the relative durations of the two subpulses. This study suggests that the transmembrane potential can be regulated using a bipolar pulsed-DC field. It also shows that the shapes admitted in the dynamics of a vesicle depend upon whether the pulse is unipolar or bipolar. Parameters are suggested wherein the simulation results can be demonstrated in experiments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Petač2021,

title = {Testing the predictions of axisymmetric distribution functions of galactic dark matter with hydrodynamical simulations},

author = {Mihael Petač and Julien Lavalle and Arturo Núñez-Castiñeyra and Emmanuel Nezri},

doi = {10.1088/1475-7516/2021/08/031},

issn = {1475-7516},

year  = {2021},

date = {2021-08-01},

journal = {J. Cosmol. Astropart. Phys.},

volume = {2021},

number = {08},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Boivin2021,

title = {Benchmarking a lattice-Boltzmann solver for reactive flows: Is the method worth the effort for combustion?},

author = {P. Boivin and M. Tayyab and S. Zhao},

doi = {10.1063/5.0057352},

issn = {1089-7666},

year  = {2021},

date = {2021-07-01},

volume = {33},

number = {7},

publisher = {AIP Publishing},

abstract = {This Letter reports a validation of a lattice-Boltzmann approach following the Taylor–Green Vortex benchmark presented at the 19th International Congress on Numerical Combustion and recently reported by Abdelsamie et al. [“The Taylor–Green vortex as a benchmark for high-fidelity combustion simulations using low-Mach solvers,” Comput. Fluids 223, 104935 (2021)]. The lattice-Boltzmann approach, despite having a time step bound by an acoustic Courant–Friedrichs–Lewy condition, provides results faster than the low-Mach solvers which performed to the benchmark. Such a feat is made possible by the fully explicit nature of the method and indicates very high potential for practical applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cai2021b,

title = {Explicit wall models for large eddy simulation},

author = {Shang-Gui Cai and Pierre Sagaut},

doi = {10.1063/5.0048563},

issn = {1089-7666},

year  = {2021},

date = {2021-04-01},

volume = {33},

number = {4},

publisher = {AIP Publishing},

abstract = {Algebraic explicit wall models covering the entire inner region of the turbulent boundary layer are proposed to reduce the computational effort for large eddy simulation of wall-bounded turbulent flows. The proposed formulas are given in closed forms with either logarithmic- or power-function-based laws of the wall, allowing straightforward evaluation of the friction velocity on near wall grids independent of their locations in the turbulent boundary layer. The performance of the proposed models is demonstrated by the wall modeled large eddy simulation of a turbulent plane channel flow.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kumar2021,

title = {Turbulent transport driven by kinetic ballooning modes in the inner core of JET hybrid H-modes},

author = {N. Kumar and Y. Camenen and S. Benkadda and C. Bourdelle and A. Loarte and A.R. Polevoi and F. Widmer and JET contributors},

doi = {10.1088/1741-4326/abd09c},

issn = {1741-4326},

year  = {2021},

date = {2021-03-01},

journal = {Nucl. Fusion},

volume = {61},

number = {3},

publisher = {IOP Publishing},

abstract = {Abstract

               Turbulent transport in the inner core of the high-β JET hybrid discharge 75225 is investigated extensively through linear and non-linear gyro-kinetic (GK) simulations using the GK code GKW in the local approximation limit. Compared to previous studies (Citrin et al 2015 Plasma Phys. Control. Fusion 

                  57 014032; Garcia et al 2015 Nucl. Fusion 

                  55 053007), the analysis has been extended towards the magnetic axis, ρ < 0.3, where the turbulence characteristics remain an open question. Understanding turbulent transport in this region is crucial to predict core profile peaking that in turn will impact the fusion reactions and the tungsten neoclassical transport, in present devices as well as in ITER. At ρ = 0.15, a linear stability analysis indicates that kinetic ballooning modes (KBMs) dominate, with an extended mode structure in ballooning space due to the low magnetic shear. The sensitivity of KBM stability to main plasma parameters is investigated. In the non-linear regime, the turbulence induced by these KBMs drives a significant ion and electron heat flux. Standard quasi-linear (QL) models are compared to the non-linear results. The standard reduced QL models work well for the E × B fluxes, but fail to capture magnetic flutter contribution to the electron heat flux induced by the non-linear excitation of low k

                  

                     θ

                  

                  ρ

                  i micro-tearing modes that are linearly stable. An extension of the QL models is proposed allowing better capturing the magnetic flutter flux.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tayyab2021,

title = {Lattice-Boltzmann modeling of a turbulent bluff-body stabilized flame},

author = {M. Tayyab and S. Zhao and P. Boivin},

doi = {10.1063/5.0038089},

issn = {1089-7666},

year  = {2021},

date = {2021-03-01},

volume = {33},

number = {3},

publisher = {AIP Publishing},

abstract = {This Letter reports the first large eddy simulation of a turbulent flame using a lattice-Boltzmann model. To that end, simulation of a bluff-body stabilized propane–air flame is carried out, showing an agreement similar to those available in the literature. Computational costs are also reported, indicating that lattice-Boltzmann modeling of reactive flows is competitive, with around 1000cpuh required to simulate one residence time in the 1.5 m burner.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Xiang2021,

title = {Buckling Bars in Nearly Face-on Galaxies Observed with MaNGA},

author = {Katherine M. Xiang and David M. Nataf and E. Athanassoula and Nadia L. Zakamska and Kate Rowlands and Karen Masters and Amelia Fraser-McKelvie and Niv Drory and Katarina Kraljic},

doi = {10.3847/1538-4357/abdab5},

issn = {1538-4357},

year  = {2021},

date = {2021-03-01},

journal = {ApJ},

volume = {909},

number = {2},

publisher = {American Astronomical Society},

abstract = {Abstract

               Over half of disk galaxies are barred, yet the mechanisms for bar formation and the lifetime of bar buckling remain poorly understood. In simulations, a thin bar undergoes a rapid (<1 Gyr) event called “buckling,” during which the inner part of the bar is asymmetrically bent out of the galaxy plane and eventually thickens, developing a peanut/X-shaped profile when viewed side-on. Through analyzing stellar kinematics of N-body model snapshots of a galaxy before, during, and after the buckling phase, we confirm a distinct quadrupolar pattern of out-of-plane stellar velocities in nearly face-on galaxies. This kinematic signature of buckling allows us to identify five candidates of currently buckling bars among 434 barred galaxies in the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) Survey, an integral field unit spectroscopic survey that measures the composition and kinematic structure of nearby galaxies. The frequency of buckling events detected is consistent with the 0.5–1 Gyr timescale predicted by simulations. The five candidates we present more than double the total number of candidate buckling bars and are the only ones found using the kinematic signature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bruekers2021,

title = {Front Cover: Allosteric Guest Binding in Chiral Zirconium(IV) Double Decker Porphyrin Cages (Eur. J. Org. Chem. 4/2021)},

author = {Jeroen P. J. Bruekers and Matthijs A. Hellinghuizen and Nicolas Vanthuyne and Paul Tinnemans and Pieter J. Gilissen and Wybren Jan Buma and Jean‐Valère Naubron and Jeanne Crassous and Johannes A. A. W. Elemans and Roeland J. M. Nolte},

doi = {10.1002/ejoc.202001599},

issn = {1099-0690},

year  = {2021},

date = {2021-01-26},

journal = {Eur J Org Chem},

volume = {2021},

number = {4},

pages = {512--512},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huix-Rotllant2021,

title = {Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome},

author = {Miquel Huix-Rotllant and Karno Schwinn and Nicolas Ferré},

doi = {10.1039/d0cp06070d},

issn = {1463-9084},

year  = {2021},

date = {2021-01-21},

journal = {Phys. Chem. Chem. Phys.},

volume = {23},

number = {2},

pages = {1666--1674},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {
Combined QM/MM Hessians and local normal mode analysis are powerful tools to simulate and interpret complex IR spectra of biological macromolecules.
},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huix-Rotllant2020,

title = {Analytic Energy, Gradient, and Hessian of Electrostatic Embedding QM/MM Based on Electrostatic Potential-Fitted Atomic Charges Scaling Linearly with the MM Subsystem Size},

author = {Miquel Huix-Rotllant and Nicolas Ferré},

doi = {10.1021/acs.jctc.0c01075},

issn = {1549-9626},

year  = {2021},

date = {2021-01-12},

journal = {J. Chem. Theory Comput.},

volume = {17},

number = {1},

pages = {538--548},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Guo2020,

title = {Improved standard thermal lattice Boltzmann model with hybrid recursive regularization for compressible laminar and turbulent flows},

author = {S. Guo and Y. Feng and P. Sagaut},

doi = {10.1063/5.0033364},

issn = {1089-7666},

year  = {2020},

date = {2020-12-01},

volume = {32},

number = {12},

publisher = {AIP Publishing},

abstract = {Based on recent work by Guo et al. [“An efficient lattice Boltzmann method for compressible aerodynamics on D3Q19 lattice,” J. Comput. Phys. 418, 109570 (2020)], an improved thermal hybrid recursive regularized lattice Boltzmann model (iHRR-ρ) on a regular lattice is developed for two- and three-dimensional compressible laminar and turbulent flows. To enhance the numerical stability in a broad range of Courant–Friedrichs–Lewy numbers and in under-resolved simulations, a new equilibrium density distribution function is proposed to enlarge its positivity region in the Mach–temperature plane. An embedded hybridizing procedure is introduced in the quasi-symmetry correction terms, which allow for a decoupled treatment of unphysical modes and physical under-resolved turbulent scales on coarse grids. To handle compressible turbulent flows, the under-resolved scales are modeled using the original hybrid recursive regularized collision model given by Jacob et al. [“A new hybrid recursive regularised Bhatnagar–Gross–Krook collision model for Lattice Boltzmann method-based large eddy simulation,” J. Turbul. 19, 1051–1076 (2018)] equipped with Vreman’s subgrid model for the large-eddy simulation. The validity and accuracy of the present method for laminar and turbulent compressible flows are assessed by considering six test cases: (I) viscous shock wave internal structure, (II) isentropic vortex convection in a supersonic regime, (III) non-isothermal acoustic pulse, (IV) vortex–shock wave interaction, (V) supersonic flow over NACA airfoil at Re = 10 000 and Ma = 1.5, and (VI) compressible Taylor–Green vortex at Ma = 0.29.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gallo2020,

title = {Interpretative transport modeling of the WEST boundary plasma: main plasma and light impurities},

author = {A. Gallo and A. Sepetys and Y. Marandet and H. Bufferand and G. Ciraolo and N. Fedorczak and S. Brezinsek and J. Bucalossi and J. Coenen and F. Clairet and Y. Corre and C. Desgranges and P. Devynck and J. Gaspar and R. Guirlet and J. Gunn and C.C. Klepper and J.-Y. Pascal and P. Tamain and E. Tsitrone and E.A. Unterberg and the WEST team},

doi = {10.1088/1741-4326/abb95b},

issn = {1741-4326},

year  = {2020},

date = {2020-12-01},

journal = {Nucl. Fusion},

volume = {60},

number = {12},

publisher = {IOP Publishing},

abstract = {Abstract

               Understanding impurity transport in tokamak plasmas is crucial to control radiative losses and material migration in future magnetic fusion reactors. In this work we deploy the SolEdge2D-EIRENE code to model the boundary plasma in a WEST discharge, satisfactorily reproducing measurements of both upstream and divertor plasma conditions. The spatial distribution of oxygen, studied here as a representative light impurity, is compared to vacuum ultraviolet spectroscopy measurements acquired with an oscillating line of sight. The simulation captures a key feature of the experiment, namely a factor of ≃2 higher oxygen brightness in the inner divertor region compared to the outer one. This spatial asymmetry in oxygen concentration is interpreted by analyzing the balance of friction forces and thermal gradient forces that the light impurity exchanges with the main plasma.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ursin2020,

title = {Amplitude and phase changes for reflected and transmitted waves from a curved interface in anisotropic media},

author = {Bjørn Ursin and Nathalie Favretto-Cristini and Paul Cristini},

doi = {10.1093/gji/ggaa456},

issn = {1365-246X},

year  = {2020},

date = {2020-11-18},

volume = {224},

number = {1},

pages = {719--737},

publisher = {Oxford University Press (OUP)},

abstract = {SUMMARYIt is well known that seismic data that have been recorded in complex geological environments must be compensated for geometrical spreading before AVO/AVA (amplitude-versus-offset/amplitude-versus-angle) analysis, in order to avoid erroneous imaging interpretation. By investigating analytically both the effect of the geometrical spreading and the effect of the reflector curvature on amplitude and phase changes for reflected and transmitted waves between anisotropic media, using ray theory, we show that these data should be compensated for interface effects as well. In order to gain insight more specifically in the focusing effect of the interface, the special case of homogeneous isotropic media separated by a curved interface of syncline type is discussed and compared to the case of a plane interface. 3-D numerical simulations of wave reflection from curved interfaces using a spectral element method validate our analytical derivations. In particular, numerical seismograms obtained at a vertical receiver array highlight that the effect of interface curvature on the reflected events is much more pronounced in a restricted area associated with the existence of caustics, which is consistent with our analytical predictions. Moreover, comparisons between the numerical and the analytical results confirm the fact that using plane-wave reflection coefficients without correction for the interface effect may lead to wrong interpretation of AVA/AVO analysis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Oujia2020,

title = {Divergence and convergence of inertial particles in high-Reynolds-number turbulence},

author = {Thibault Oujia and Keigo Matsuda and Kai Schneider},

doi = {10.1017/jfm.2020.672},

issn = {1469-7645},

year  = {2020},

date = {2020-10-26},

journal = {J. Fluid Mech.},

volume = {905},

publisher = {Cambridge University Press (CUP)},

abstract = {Abstract

	  

	    

	      

	    

	  },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lacroix2020,

title = {Predicting the dark matter velocity distribution in galactic structures: tests against hydrodynamic cosmological simulations},

author = {Thomas Lacroix and Arturo Núñez-Castiñeyra and Martin Stref and Julien Lavalle and Emmanuel Nezri},

doi = {10.1088/1475-7516/2020/10/031},

issn = {1475-7516},

year  = {2020},

date = {2020-10-01},

journal = {J. Cosmol. Astropart. Phys.},

volume = {2020},

number = {10},

pages = {031--031},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kossoski2020,

title = {Nonadiabatic dynamics in multidimensional complex potential energy surfaces},

author = {Fábris Kossoski and Mario Barbatti},

doi = {10.1039/d0sc04197a},

issn = {2041-6539},

year  = {2020},

date = {2020-09-23},

journal = {Chem. Sci.},

volume = {11},

number = {36},

pages = {9827--9835},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {
Despite the continuous development of methods for describing nonadiabatic dynamics, there is a lack of multidimensional approaches for processes where the wave function norm is not conserved. A new surface hopping variant closes this knowledge gap.
},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krug2020,

title = {The Impact of Aggregation on the Photophysics of Spiro‐Bridged Heterotriangulenes},

author = {Marcel Krug and Maximilian Wagner and Tobias A. Schaub and Wen‐Shan Zhang and Christoph M. Schüßlbauer and Johannes D. R. Ascherl and Peter W. Münich and Rasmus R. Schröder and Franziska Gröhn and Pavlo O. Dral and Mario Barbatti and Dirk M. Guldi and Milan Kivala},

doi = {10.1002/anie.202003504},

issn = {1521-3773},

year  = {2020},

date = {2020-09-07},

journal = {Angew Chem Int Ed},

volume = {59},

number = {37},

pages = {16233--16240},

publisher = {Wiley},

abstract = {AbstractWe report on the impact of the central heteroatom on structural, electronic, and spectroscopic properties of a series of spirofluorene‐bridged heterotriangulenes and provide a detailed study on their aggregates. The in‐depth analysis of their molecular structure by NMR spectroscopy and X‐ray crystallography was further complemented by density functional theory calculations. With the aid of extensive photophysical analysis the complex fluorescence spectra were deconvoluted showing contributions from the peripheral fluorenes and the heteroaromatic cores. Beyond the molecular scale, we examined the aggregation behavior of these heterotriangulenes in THF/H2O mixtures and analyzed the aggregates by static and dynamic light scattering. The excited‐state interactions within the aggregates were found to be similar to those found in the solid state. A plethora of morphologies and superstructures were observed by scanning electron microscopy of drop‐casted dispersions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Attaf2020,

title = {Corrigendum: FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells},

author = {Noudjoud Attaf and Iñaki Cervera-Marzal and Chuang Dong and Laurine Gil and Amédée Renand and Lionel Spinelli and Pierre Milpied},

doi = {10.3389/fimmu.2020.02047},

issn = {1664-3224},

year  = {2020},

date = {2020-09-03},

journal = {Front. Immunol.},

volume = {11},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schwinn2020,

title = {UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein},

author = {Karno Schwinn and Nicolas Ferré and Miquel Huix-Rotllant},

doi = {10.1039/d0cp01714k},

issn = {1463-9084},

year  = {2020},

date = {2020-06-10},

journal = {Phys. Chem. Chem. Phys.},

volume = {22},

number = {22},

pages = {12447--12455},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {
Simulation of UV-vis absorption spectra of cryptochromes and flavoproteins requires an explicit account of vibrations of the flavin chromophore embedded in protein.
},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schwinn2020b,

title = {Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome},

author = {Karno Schwinn and Nicolas Ferré and Miquel Huix-Rotllant},

doi = {10.1021/acs.jctc.9b01145},

issn = {1549-9626},

year  = {2020},

date = {2020-06-09},

journal = {J. Chem. Theory Comput.},

volume = {16},

number = {6},

pages = {3816--3824},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Favier2020,

title = {Robust wall states in rapidly rotating Rayleigh–Bénard convection},

author = {Benjamin Favier and Edgar Knobloch},

doi = {10.1017/jfm.2020.310},

issn = {1469-7645},

year  = {2020},

date = {2020-05-11},

journal = {J. Fluid Mech.},

volume = {895},

publisher = {Cambridge University Press (CUP)},

abstract = {

	    

	      

	    

	  },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Siddique2020,

title = {Nonadiabatic Dynamics of Charge-Transfer States Using the Anthracene–Tetracyanoethylene Complex as a Prototype},

author = {Farhan Siddique and Mario Barbatti and Zhonghua Cui and Hans Lischka and Adelia J. A. Aquino},

doi = {10.1021/acs.jpca.0c01900},

issn = {1520-5215},

year  = {2020},

date = {2020-04-30},

journal = {J. Phys. Chem. A},

volume = {124},

number = {17},

pages = {3347--3357},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2020,

title = {Suppressed or Enhanced Central Star Formation Rates in Late-type Barred Galaxies},

author = {Jing Wang and E. Athanassoula and Si-Yue Yu and Christian Wolf and Li Shao and Hua Gao and T. H. Randriamampandry},

doi = {10.3847/1538-4357/ab7fad},

issn = {1538-4357},

year  = {2020},

date = {2020-04-10},

journal = {ApJ},

volume = {893},

number = {1},

publisher = {American Astronomical Society},

abstract = {Abstract

               Bars in disk-dominated galaxies are able to drive gas inflow inside the corotation radius, thus enhancing the central star formation rate (SFR). Previous work, however, has found that disk-dominated galaxies with centrally suppressed SFRs frequently host a bar. Here we investigate possible causes for the suppression of central SFRs in such cases. We compare the physical properties of a sample of disk-dominated barred galaxies with high central SFRs (HC galaxies) with those of a sample of disk-dominated barred galaxies with low central SFRs (LC galaxies). We find that the two samples have, on average, similar H i content and bars of similar strength. But we also find that the HCs have bluer colors than the LCs, and that outside the bar region, they host stronger spiral arms than the LCs, where closed rings are more often seen. We discuss and evaluate the possible causes for the suppression of the central SFR in the LC galaxies as opposed to its enhancement in the HC galaxies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jiang2020,

title = {First-principles calculations on CuInSe_{2}/AlP heterostructures},

author = {Pingping Jiang and Marie-Christine Record and Pascal Boulet},

doi = {10.1039/d0tc00131g},

issn = {2050-7534},

year  = {2020},

date = {2020-04-09},

journal = {J. Mater. Chem. C},

volume = {8},

number = {14},

pages = {4732--4742},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {
Heterostructures based on a CuInSe_{2}absorber with an AlP buffer have a 12 meV conduction band offset and achieved 27.39% of conversion efficiency.
},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lischka2020,

title = {The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry},

author = {Hans Lischka and Ron Shepard and Thomas Müller and Péter G. Szalay and Russell M. Pitzer and Adelia J. A. Aquino and Mayzza M. Araújo do Nascimento and Mario Barbatti and Lachlan T. Belcher and Jean-Philippe Blaudeau and Itamar Borges and Scott R. Brozell and Emily A. Carter and Anita Das and Gergely Gidofalvi and Leticia González and William L. Hase and Gary Kedziora and Miklos Kertesz and Fábris Kossoski and Francisco B. C. Machado and Spiridoula Matsika and Silmar A. do Monte and Dana Nachtigallová and Reed Nieman and Markus Oppel and Carol A. Parish and Felix Plasser and Rene F. K. Spada and Eric A. Stahlberg and Elizete Ventura and David R. Yarkony and Zhiyong Zhang},

doi = {10.1063/1.5144267},

issn = {1089-7690},

year  = {2020},

date = {2020-04-07},

volume = {152},

number = {13},

publisher = {AIP Publishing},

abstract = {The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nespoli2020,

title = {A new mechanism for filament disconnection at the X-point: poloidal shear in radial E × B velocity},

author = {F. Nespoli and P. Tamain and N. Fedorczak and D. Galassi and Y. Marandet},

doi = {10.1088/1741-4326/ab6f1e},

issn = {1741-4326},

year  = {2020},

date = {2020-04-01},

journal = {Nucl. Fusion},

volume = {60},

number = {4},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Maget2019,

title = {Natural poloidal asymmetry and neoclassical transport of impurities in tokamak plasmas},

author = {Patrick Maget and Judith Frank and Timothée Nicolas and Olivier Agullo and Xavier Garbet and Hinrich Lütjens},

doi = {10.1088/1361-6587/ab53ab},

issn = {1361-6587},

year  = {2020},

date = {2020-02-01},

journal = {Plasma Phys. Control. Fusion},

volume = {62},

number = {2},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Karageorgi2019,

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 = {1476-4687},

year  = {2019},

date = {2019-10-17},

journal = {Nature},

volume = {574},

number = {7778},

pages = {409--412},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jiang2019,

title = {A DFT study of the electronic, optical and topological properties of free and biaxially strained CuIn_{1−x}Al_{x}Se_{2}},

author = {Pingping Jiang and Pascal Boulet and Marie-Christine Record},

doi = {10.1039/c9tc00277d},

issn = {2050-7534},

year  = {2019},

date = {2019-05-16},

journal = {J. Mater. Chem. C},

volume = {7},

number = {19},

pages = {5803--5815},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {
Among the CuIn_{1−x}Al_{x}Se_{2}alloys, that withx= 0.25 is the optimal one in terms of band gap and conversion efficiency. Its absorption coefficient is highly modified under biaxial strains that occur in thin films.
},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chown2019,

title = {Linking bar- and interaction-driven molecular gas concentration with centrally enhanced star formation in EDGE–CALIFA galaxies},

author = {Ryan Chown and Cheng Li and E Athanassoula and Niu Li and Christine D Wilson and Lin Lin and Houjun Mo and Laura C Parker and Ting Xiao},

doi = {10.1093/mnras/stz349},

issn = {1365-2966},

year  = {2019},

date = {2019-04-21},

volume = {484},

number = {4},

pages = {5192--5211},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2019,

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},

doi = {10.1021/acs.jpclett.9b00286},

issn = {1948-7185},

year  = {2019},

date = {2019-03-21},

journal = {J. Phys. Chem. Lett.},

volume = {10},

number = {6},

pages = {1388--1393},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PereiraRodrigues2019,

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},

doi = {10.1021/acs.jpca.8b12482},

issn = {1520-5215},

year  = {2019},

date = {2019-03-14},

journal = {J. Phys. Chem. A},

volume = {123},

number = {10},

pages = {1953--1961},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bai2019,

title = {Mechanism of Spin-Exchange Internal Conversion: Practical Proxies for Diabatic and Nonadiabatic Couplings},

author = {Shuming Bai and Mario Barbatti},

doi = {10.1021/acs.jctc.8b00923},

issn = {1549-9626},

year  = {2019},

date = {2019-03-12},

journal = {J. Chem. Theory Comput.},

volume = {15},

number = {3},

pages = {1503--1513},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Denawi2019,

title = {Magnetic Polymer Chains of Transition Metal Atoms and Zwitterionic Quinone},

author = {Hassan Denawi and Mathieu Abel and Roland Hayn},

doi = {10.1021/acs.jpcc.8b12433},

issn = {1932-7455},

year  = {2019},

date = {2019-02-21},

journal = {J. Phys. Chem. C},

volume = {123},

number = {7},

pages = {4582--4589},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cavassilas2018,

title = {Dual-Gated WTe_{2}/MoSe_{2} van der Waals Tandem Solar Cells},

author = {Nicolas Cavassilas and Demetrio Logoteta and Youseung Lee and Fabienne Michelini and Michel Lannoo and Marc Bescond and Mathieu Luisier},

doi = {10.1021/acs.jpcc.8b09905},

issn = {1932-7455},

year  = {2018},

date = {2018-12-20},

journal = {J. Phys. Chem. C},

volume = {122},

number = {50},

pages = {28545--28549},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rocco2018b,

title = {High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes},

author = {M. L. M. Rocco and M. Häming and C. E. V. de Moura and M. Barbatti and A. B. Rocha and A. Schöll and E. Umbach},

doi = {10.1021/acs.jpcc.8b08945},

issn = {1932-7455},

year  = {2018},

date = {2018-12-20},

journal = {J. Phys. Chem. C},

volume = {122},

number = {50},

pages = {28692--28701},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rocco2018,

title = {High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes},

author = {M. L. M. Rocco and M. Häming and C. E. V. de Moura and M. Barbatti and A. B. Rocha and A. Schöll and E. Umbach},

doi = {10.1021/acs.jpcc.8b08945},

issn = {1932-7455},

year  = {2018},

date = {2018-12-20},

journal = {J. Phys. Chem. C},

volume = {122},

number = {50},

pages = {28692--28701},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ješko2018,

title = {Studying divertor relevant plasmas in the Pilot-PSI linear plasma device: experiments versus modelling},

author = {K Ješko and Y Marandet and H Bufferand and J P Gunn and H J van der Meiden and G Ciraolo},

doi = {10.1088/1361-6587/aae80d},

issn = {1361-6587},

year  = {2018},

date = {2018-12-01},

journal = {Plasma Phys. Control. Fusion},

volume = {60},

number = {12},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Favier2018,

title = {Rayleigh–Bénard convection with a melting boundary},

author = {B. Favier and J. Purseed and L. Duchemin},

doi = {10.1017/jfm.2018.773},

issn = {1469-7645},

year  = {2018},

date = {2018-11-06},

journal = {J. Fluid Mech.},

volume = {858},

pages = {437--473},

publisher = {Cambridge University Press (CUP)},

abstract = {We study the evolution of a melting front between the solid and liquid phases of a pure incompressible material where fluid motions are driven by unstable temperature gradients. In a plane-layer geometry, this can be seen as classical Rayleigh–Bénard convection where the upper solid boundary is allowed to melt due to the heat flux brought by the fluid underneath. This free-boundary problem is studied numerically in two dimensions using a phase-field approach, classically used to study the melting and solidification of alloys, which we dynamically couple with the Navier–Stokes equations in the Boussinesq approximation. The advantage of this approach is that it requires only moderate modifications of classical numerical methods. We focus on the case where the solid is initially nearly isothermal, so that the evolution of the topography is related to the inhomogeneous heat flux from thermal convection, and does not depend on the conduction problem in the solid. From a very thin stable layer of fluid, convection cells appear as the depth – and therefore the effective Rayleigh number – of the layer increases. The continuous melting of the solid leads to dynamical transitions between different convection cell sizes and topography amplitudes. The Nusselt number can be larger than its value for a planar upper boundary, due to the feedback of the topography on the flow, which can stabilize large-scale laminar convection cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{David2018,

title = {Chemical Tuning of Magnetic Exchange Couplings Using Broken-Symmetry Density Functional Theory},

author = {Grégoire David and Frank Wennmohs and Frank Neese and Nicolas Ferré},

doi = {10.1021/acs.inorgchem.8b01970},

issn = {1520-510X},

year  = {2018},

date = {2018-10-15},

journal = {Inorg. Chem.},

volume = {57},

number = {20},

pages = {12769--12776},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dral2018,

title = {Nonadiabatic Excited-State Dynamics with Machine Learning},

author = {Pavlo O. Dral and Mario Barbatti and Walter Thiel},

doi = {10.1021/acs.jpclett.8b02469},

issn = {1948-7185},

year  = {2018},

date = {2018-10-04},

journal = {J. Phys. Chem. Lett.},

volume = {9},

number = {19},

pages = {5660--5663},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{deMedeiros2018,

title = {Photochemistry of CF_{3}Cl: Quenching of Charged Fragments Is Caused by Nonadiabatic Effects},

author = {Vanessa C. de Medeiros and Railton B. de Andrade and Gessenildo P. Rodrigues and Glauco F. Bauerfeldt and Elizete Ventura and Mario Barbatti and Silmar A. do Monte},

doi = {10.1021/acs.jctc.8b00457},

issn = {1549-9626},

year  = {2018},

date = {2018-09-11},

journal = {J. Chem. Theory Comput.},

volume = {14},

number = {9},

pages = {4844--4855},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bottero2018,

title = {Broadband transmission losses and time dispersion maps from time-domain numerical simulations in ocean acoustics},

author = {Alexis Bottero and Paul Cristini and Dimitri Komatitsch and Quentin Brissaud},

doi = {10.1121/1.5055787},

issn = {1520-8524},

year  = {2018},

date = {2018-09-01},

volume = {144},

number = {3},

pages = {EL222--EL228},

publisher = {Acoustical Society of America (ASA)},

abstract = {In this letter, a procedure for the calculation of transmission loss maps from numerical simulations in the time domain is presented. It can be generalized to arbitrary time sequences and to elastic media and provides an insight into how energy spreads into a complex configuration. In addition, time dispersion maps can be generated. These maps provide additional information on how energy is distributed over time. Transmission loss and time dispersion maps are generated at a negligible additional computational cost. To illustrate the type of transmission loss maps that can be produced by the time-domain method, the problem of the classical two-dimensional upslope wedge with a fluid bottom is addressed. The results obtained are compared to those obtained previously based on a parabolic equation. Then, for the same configuration, maps for an elastic bottom and maps for non-monochromatic signals are computed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lischka2018,

title = {Multireference Approaches for Excited States of Molecules},

author = {Hans Lischka and Dana Nachtigallová and Adélia J. A. Aquino and Péter G. Szalay and Felix Plasser and Francisco B. C. Machado and Mario Barbatti},

doi = {10.1021/acs.chemrev.8b00244},

issn = {1520-6890},

year  = {2018},

date = {2018-08-08},

journal = {Chem. Rev.},

volume = {118},

number = {15},

pages = {7293--7361},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Crespo-Otero2018,

title = {Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics},

author = {Rachel Crespo-Otero and Mario Barbatti},

doi = {10.1021/acs.chemrev.7b00577},

issn = {1520-6890},

year  = {2018},

date = {2018-08-08},

journal = {Chem. Rev.},

volume = {118},

number = {15},

pages = {7026--7068},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kossoski2018,

title = {Nuclear Ensemble Approach with Importance Sampling},

author = {Fábris Kossoski and Mario Barbatti},

doi = {10.1021/acs.jctc.8b00059},

issn = {1549-9626},

year  = {2018},

date = {2018-06-12},

journal = {J. Chem. Theory Comput.},

volume = {14},

number = {6},

pages = {3173--3183},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cabanes2018,

title = {Some statistical properties of three-dimensional zonostrophic turbulence},

author = {S. Cabanes and B. Favier and M. Le Bars},

doi = {10.1080/03091929.2018.1467413},

issn = {1029-0419},

year  = {2018},

date = {2018-05-04},

journal = {Geophysical & Astrophysical Fluid Dynamics},

volume = {112},

number = {3},

pages = {207--221},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{García-Iriepa2018,

title = {Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water},

author = {Cristina García-Iriepa and Pauline Gosset and Romain Berraud-Pache and Madjid Zemmouche and Grégory Taupier and Kokou Dodzi Dorkenoo and Pascal Didier and Jérémie Léonard and Nicolas Ferré and Isabelle Navizet},

doi = {10.1021/acs.jctc.7b01240},

issn = {1549-9626},

year  = {2018},

date = {2018-04-10},

journal = {J. Chem. Theory Comput.},

volume = {14},

number = {4},

pages = {2117--2126},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chateau2018,

title = {Transport and Mixing Induced by Beating Cilia in Human Airways},

author = {Sylvain Chateau and Umberto D'Ortona and Sébastien Poncet and Julien Favier},

doi = {10.3389/fphys.2018.00161},

issn = {1664-042X},

year  = {2018},

date = {2018-03-06},

journal = {Front. Physiol.},

volume = {9},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Reddy2018,

title = {Turbulent Kinematic Dynamos in Ellipsoids Driven by Mechanical Forcing},

author = {K. Sandeep Reddy and Benjamin Favier and Michael Le Bars},

doi = {10.1002/2017gl076542},

issn = {1944-8007},

year  = {2018},

date = {2018-02-28},

journal = {Geophysical Research Letters},

volume = {45},

number = {4},

pages = {1741--1750},

publisher = {American Geophysical Union (AGU)},

abstract = {AbstractDynamo action in planetary cores has been extensively studied in the context of convectively driven flows. We show in this letter that mechanical forcings, namely, tides, libration, and precession, are also able to kinematically sustain a magnetic field against ohmic diffusion. Previous attempts published in the literature focused on the laminar response or considered idealized spherical configurations. In contrast, we focus here on the developed turbulent regime and we self‐consistently solve the magnetohydrodynamic equations in an ellipsoidal container. Our results open new avenues of research in dynamo theory where both convection and mechanical forcing can play a role, independently or simultaneously.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LeReun2018,

title = {Parametric instability and wave turbulence driven by tidal excitation of internal waves},

author = {Thomas Le Reun and Benjamin Favier and Michael Le Bars},

doi = {10.1017/jfm.2018.18},

issn = {1469-7645},

year  = {2018},

date = {2018-02-14},

journal = {J. Fluid Mech.},

volume = {840},

pages = {498--529},

publisher = {Cambridge University Press (CUP)},

abstract = {We investigate the stability of stratified fluid layers undergoing homogeneous and periodic tidal deformation. We first introduce a local model which allows us to study velocity and buoyancy fluctuations in a Lagrangian domain periodically stretched and sheared by the tidal base flow. While keeping the key physical ingredients only, such a model is efficient in simulating planetary regimes where tidal amplitudes and dissipation are small. With this model, we prove that tidal flows are able to drive parametric subharmonic resonances of internal waves, in a way reminiscent of the elliptical instability in rotating fluids. The growth rates computed via direct numerical simulations (DNSs) are in very good agreement with Wentzel–Kramers–Brillouin analysis and Floquet theory. We also investigate the turbulence driven by this instability mechanism. With spatio-temporal analysis, we show that it is weak internal wave turbulence occurring at small Froude and buoyancy Reynolds numbers. When the gap between the excitation and the Brunt–Väisälä frequencies is increased, the frequency spectrum of this wave turbulence displays a $-2$ power law reminiscent of the high-frequency branch of the Garett and Munk spectrum (Geophys. Fluid Dyn., vol. 3 (1), 1972, pp. 225–264) which has been measured in the oceans. In addition, we find that the mixing efficiency is altered compared to what is computed in the context of DNS of stratified turbulence excited at small Froude and large buoyancy Reynolds numbers and is consistent with a superposition of waves.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Stojanović2017,

title = {Nonadiabatic Dynamics of Cycloparaphenylenes with TD-DFTB Surface Hopping},

author = {Ljiljana Stojanović and Saadullah G. Aziz and Rifaat H. Hilal and Felix Plasser and Thomas A. Niehaus and Mario Barbatti},

doi = {10.1021/acs.jctc.7b01000},

issn = {1549-9626},

year  = {2017},

date = {2017-12-12},

journal = {J. Chem. Theory Comput.},

volume = {13},

number = {12},

pages = {5846--5860},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bai2017b,

title = {Divide-to-Conquer: A Kinetic Model for Singlet Oxygen Photosensitization},

author = {Shuming Bai and Mario Barbatti},

doi = {10.1021/acs.jctc.7b00619},

issn = {1549-9626},

year  = {2017},

date = {2017-11-14},

journal = {J. Chem. Theory Comput.},

volume = {13},

number = {11},

pages = {5528--5538},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bai2017,

title = {Spatial Factors for Triplet Fusion Reaction of Singlet Oxygen Photosensitization},

author = {Shuming Bai and Mario Barbatti},

doi = {10.1021/acs.jpclett.7b02574},

issn = {1948-7185},

year  = {2017},

date = {2017-11-02},

journal = {J. Phys. Chem. Lett.},

volume = {8},

number = {21},

pages = {5456--5460},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fazzi2017,

title = {Hot and Cold Charge-Transfer Mechanisms in Organic Photovoltaics: Insights into the Excited States of Donor/Acceptor Interfaces},

author = {Daniele Fazzi and Mario Barbatti and Walter Thiel},

doi = {10.1021/acs.jpclett.7b02144},

issn = {1948-7185},

year  = {2017},

date = {2017-10-05},

journal = {J. Phys. Chem. Lett.},

volume = {8},

number = {19},

pages = {4727--4734},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Athanassoula2016,

title = {Metallicity-dependent kinematics and morphology of the Milky Way bulge},

author = {E. Athanassoula and S. A. Rodionov and N. Prantzos},

doi = {10.1093/mnrasl/slw255},

issn = {1745-3933},

year  = {2017},

date = {2017-05-01},

volume = {467},

number = {1},

pages = {L46--L50},

publisher = {Oxford University Press (OUP)},

abstract = {Abstract

               We use N-body chemo-dynamic simulations to study the coupling between morphology, kinematics and metallicity of the bar/bulge region of our Galaxy. We make qualitative comparisons of our results with available observations and find very good agreement. We conclude that this region is complex, since it comprises several stellar components with different properties – i.e. a boxy/peanut bulge, thin and thick disc components, and, to lesser extents, a disky pseudo-bulge, a stellar halo and a small classical bulge – all cohabiting in dynamical equilibrium. Our models show strong links between kinematics and metallicity, or morphology and metallicity, as already suggested by a number of recent observations. We discuss and explain these links.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Agullo2017,

title = {Nonlinear dynamics of turbulence driven magnetic islands. II. Numerical simulations},

author = {O. Agullo and M. Muraglia and S. Benkadda and A. Poyé and N. Dubuit and X. Garbet and A. Sen},

doi = {10.1063/1.4981230},

issn = {1089-7674},

year  = {2017},

date = {2017-04-01},

volume = {24},

number = {4},

publisher = {AIP Publishing},

abstract = {The nonlinear dynamics of a turbulence driven magnetic island (TDMI) is investigated numerically in a reduced magnetohydrodynamic fluid model. The significance of identifying a characteristic signature of a TDMI for its experimental observation is discussed. The principal focus of our simulations is on the nature of the pressure profile flattening inside a TDMI, and we show that, in agreement with analytical predictions, a partial flattening occurs when the island size exceeds a critical value that is a function of the small scale interchange dynamics. We also present a model and test it numerically, which links explicitly the interchange turbulence and the island pressure flattening.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Agullo2017b,

title = {Nonlinear dynamics of turbulence driven magnetic islands. I. Theoretical aspects},

author = {O. Agullo and M. Muraglia and S. Benkadda and A. Poyé and N. Dubuit and X. Garbet and A. Sen},

doi = {10.1063/1.4981229},

issn = {1089-7674},

year  = {2017},

date = {2017-04-01},

volume = {24},

number = {4},

publisher = {AIP Publishing},

abstract = {The nonlinear properties of a turbulence driven magnetic island (TDMI) are investigated. Starting from a minimal magnetohydrodynamic fluid model that provides for the generation of a TDMI and using scale separation arguments along with numerical simulation findings, we elucidate the links between the nonlinear transport properties of such magnetic islands and the characteristic features of the small scale turbulence. We also explain the phenomenon of partial pressure flattening inside the TDMI.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rodionov2017,

title = {Forming disk galaxies in major mergers},

author = {S. A. Rodionov and E. Athanassoula and N. Peschken},

doi = {10.1051/0004-6361/201628319},

issn = {1432-0746},

year  = {2017},

date = {2017-03-22},

journal = {A&A},

volume = {600},

publisher = {EDP Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gao2017,

title = {Evaluation of Spin-Orbit Couplings with Linear-Response Time-Dependent Density Functional Methods},

author = {Xing Gao and Shuming Bai and Daniele Fazzi and Thomas Niehaus and Mario Barbatti and Walter Thiel},

doi = {10.1021/acs.jctc.6b00915},

issn = {1549-9626},

year  = {2017},

date = {2017-02-14},

journal = {J. Chem. Theory Comput.},

volume = {13},

number = {2},

pages = {515--524},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{KANDASKALOV2017278b,

title = {A first-principle study of the structural, elastic, lattice dynamical and thermodynamic properties of a''-e16C2 and a''-Fe16N2 phases},

author = {Dmytro Kandaskalov and Philippe Maugis},

url = {https://www.sciencedirect.com/science/article/pii/S0927025616305730},

doi = {https://doi.org/10.1016/j.commatsci.2016.11.022},

issn = {0927-0256},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Computational Materials Science},

volume = {128},

pages = {278-286},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grannan2016,

title = {Tidally-forced turbulence in planetary interiors},

author = {A. M. Grannan and B. Favier and M. Le Bars and J. M. Aurnou},

doi = {10.1093/gji/ggw479},

issn = {1365-246X},

year  = {2016},

date = {2016-12-23},

journal = {Geophys. J. Int.},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2016,

title = {Orbital classification in an\textit{N}-body bar},

author = {Yougang Wang and E. Athanassoula and Shude Mao},

doi = {10.1093/mnras/stw2301},

issn = {1365-2966},

year  = {2016},

date = {2016-12-21},

journal = {Mon. Not. R. Astron. Soc.},

volume = {463},

number = {4},

pages = {3499--3512},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Stojanović2016b,

title = {UV excitations of halons},

author = {Ljiljana Stojanović and Abdulrahman O. Alyoubi and Saadullah G. Aziz and Rifaat H. Hilal and Mario Barbatti},

doi = {10.1063/1.4967170},

issn = {1089-7690},

year  = {2016},

date = {2016-11-14},

volume = {145},

number = {18},

publisher = {AIP Publishing},

abstract = {In the present study, we examined the UV excitations of a newly introduced molecular set, Halons-9, composed of nine gaseous halon molecules. The performance of the density functional-based multi-reference configuration interaction method (DFT/MRCI) and time-dependent density functional theory with CAM-B3LYP functional (TD-CAM-B3LYP) in the computation of singlet and triplet excited states of this set was evaluated against coupled-cluster with singles and doubles (CCSD). Excited states up to the corresponding ionization limits, including both localized and delocalized excitations, have been benchmarked. TD-CAM-B3LYP significantly underestimates excitation energies of the higher mixed valence-Rydberg and Rydberg states, with computed mean absolute deviations from the equation of motion (EOM)-CCSD results 1.06 and 0.76 eV, respectively. DFT/MRCI gives a significantly better description of higher excited states, albeit still poor, compared to the TD-CAM-B3LYP. The mean absolute deviations of mixed valence-Rydberg and Rydberg states from the reference EOM-CCSD values are 0.66 and 0.47 eV, respectively. The performance of DFT/MRCI for description of strongly correlated states with valence-Rydberg mixing is still not satisfactory enough. On the other hand, oscillator strengths of most of singlet states obtained with both methods are close to the EOM-CCSD values. The largest deviations, occurring in the case of several high-lying multiconfigurational states, are of an order of magnitude.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kim2016,

title = {Evidence of bar-induced secular evolution in the inner regions of stellar discs in galaxies: what shapes disc galaxies?},

author = {Taehyun Kim and Dimitri A. Gadotti and E. Athanassoula and Albert Bosma and Kartik Sheth and Myung Gyoon Lee},

doi = {10.1093/mnras/stw1899},

issn = {1365-2966},

year  = {2016},

date = {2016-11-11},

journal = {Mon. Not. R. Astron. Soc.},

volume = {462},

number = {4},

pages = {3430--3440},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bottero2016,

title = {An axisymmetric time-domain spectral-element method for full-wave simulations: Application to ocean acoustics},

author = {Alexis Bottero and Paul Cristini and Dimitri Komatitsch and Mark Asch},

doi = {10.1121/1.4965964},

issn = {1520-8524},

year  = {2016},

date = {2016-11-01},

volume = {140},

number = {5},

pages = {3520--3530},

publisher = {Acoustical Society of America (ASA)},

abstract = {The numerical simulation of acoustic waves in complex three-dimensional (3D) media is a key topic in many branches of science, from exploration geophysics to non-destructive testing and medical imaging. With the drastic increase in computing capabilities this field has dramatically grown in the last 20 years. However many 3D computations, especially at high frequency and/or long range, are still far beyond current reach and force researchers to resort to approximations, for example, by working in two dimensions (plane strain) or by using a paraxial approximation. This article presents and validates a numerical technique based on an axisymmetric formulation of a spectral finite-element method in the time domain for heterogeneous fluid-solid media. Taking advantage of axisymmetry enables the study of relevant 3D configurations at a very moderate computational cost. The axisymmetric spectral-element formulation is first introduced, and validation tests are then performed. A typical application of interest in ocean acoustics showing upslope propagation above a dipping viscoelastic ocean bottom is then presented. The method correctly models backscattered waves and explains the transmission losses discrepancies pointed out in F. B. Jensen, P. L. Nielsen, M. Zampolli, M. D. Collins, and W. L. Siegmann, Proceedings of the 8th International Conference on Theoretical and Computational Acoustics (ICTCA) (2007). Finally, a realistic application to a double seamount problem is considered.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Arbelo-González2016,

title = {Steady and Time-Resolved Photoelectron Spectra Based on Nuclear Ensembles},

author = {Wilmer Arbelo-González and Rachel Crespo-Otero and Mario Barbatti},

doi = {10.1021/acs.jctc.6b00704},

issn = {1549-9626},

year  = {2016},

date = {2016-10-11},

journal = {J. Chem. Theory Comput.},

volume = {12},

number = {10},

pages = {5037--5049},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huix-Rotllant2016b,

title = {An Effective Procedure for Analyzing Molecular Vibrations in Terms of Local Fragment Modes},

author = {Miquel Huix-Rotllant and Nicolas Ferré},

doi = {10.1021/acs.jctc.6b00514},

issn = {1549-9626},

year  = {2016},

date = {2016-10-11},

journal = {J. Chem. Theory Comput.},

volume = {12},

number = {10},

pages = {4768--4777},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Antol2016,

title = {Insights on the Auxochromic Properties of the Guanidinium Group},

author = {Ivana Antol and Zoran Glasovac and Davor Margetić and Rachel Crespo-Otero and Mario Barbatti},

doi = {10.1021/acs.jpca.6b05180},

issn = {1520-5215},

year  = {2016},

date = {2016-09-15},

journal = {J. Phys. Chem. A},

volume = {120},

number = {36},

pages = {7088--7100},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bai2016,

title = {Why Replacing Different Oxygens of Thymine with Sulfur Causes Distinct Absorption and Intersystem Crossing},

author = {Shuming Bai and Mario Barbatti},

doi = {10.1021/acs.jpca.6b05110},

issn = {1520-5215},

year  = {2016},

date = {2016-08-18},

journal = {J. Phys. Chem. A},

volume = {120},

number = {32},

pages = {6342--6350},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Xie2016,

title = {A perfectly matched layer for fluid-solid problems: Application to ocean-acoustics simulations with solid ocean bottoms},

author = {Zhinan Xie and René Matzen and Paul Cristini and Dimitri Komatitsch and Roland Martin},

doi = {10.1121/1.4954736},

issn = {1520-8524},

year  = {2016},

date = {2016-07-01},

volume = {140},

number = {1},

pages = {165--175},

publisher = {Acoustical Society of America (ASA)},

abstract = {A time-domain Legendre spectral-element method is described for full-wave simulation of ocean acoustics models, i.e., coupled fluid-solid problems in unbounded or semi-infinite domains, taking into account shear wave propagation in the ocean bottom. The technique can accommodate range-dependent and depth-dependent wave speed and density, as well as steep ocean floor topography. For truncation of the infinite domain, to efficiently absorb outgoing waves, a fluid-solid complex-frequency-shifted unsplit perfectly matched layer is introduced based on the complex coordinate stretching technique. The complex stretching is rigorously taken into account in the derivation of the fluid-solid matching condition inside the absorbing layer, which has never been done before in the time domain. Two implementations are designed: a convolutional formulation and an auxiliary differential equation formulation because the latter allows for implementation of high-order time schemes, leading to reduced numerical dispersion and dissipation, a topic of importance, in particular, in long-range ocean acoustics simulations. The method is validated for a two dimensional fluid-solid Pekeris waveguide and for a three dimensional seamount model, which shows that the technique is accurate and numerically long-time stable. Compared with widely used paraxial absorbing boundary conditions, the perfectly matched layer is significantly more efficient at absorbing both body waves and interface waves.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fazzi2016,

title = {Unveiling the Role of \textit{Hot} Charge-Transfer States in Molecular Aggregates via Nonadiabatic Dynamics},

author = {Daniele Fazzi and Mario Barbatti and Walter Thiel},

doi = {10.1021/jacs.5b13210},

issn = {1520-5126},

year  = {2016},

date = {2016-04-06},

journal = {J. Am. Chem. Soc.},

volume = {138},

number = {13},

pages = {4502--4511},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jauzac2016,

title = {Hubble Frontier Fields: predictions for the return of SN Refsdal with the MUSE and GMOS spectrographs},

author = {M. Jauzac and J. Richard and M. Limousin and K. Knowles and G. Mahler and G. P. Smith and J.-P. Kneib and E. Jullo and P. Natarajan and H. Ebeling and H. Atek and B. Clément and D. Eckert and E. Egami and R. Massey and M. Rexroth},

doi = {10.1093/mnras/stw069},

issn = {1365-2966},

year  = {2016},

date = {2016-04-01},

journal = {Mon. Not. R. Astron. Soc.},

volume = {457},

number = {2},

pages = {2029--2042},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gounley2016,

title = {Influence of surface viscosity on droplets in shear flow},

author = {J. Gounley and G. Boedec and M. Jaeger and M. Leonetti},

doi = {10.1017/jfm.2016.39},

issn = {1469-7645},

year  = {2016},

date = {2016-02-22},

journal = {J. Fluid Mech.},

volume = {791},

pages = {464--494},

publisher = {Cambridge University Press (CUP)},

abstract = {The behaviour of a single droplet in an immiscible external fluid, submitted to shear flow is investigated using numerical simulations. The surface of the droplet is modelled by a Boussinesq–Scriven constitutive law involving the interfacial viscosities and a constant surface tension. A numerical method using Loop subdivision surfaces to represent droplet interface is introduced. This method couples boundary element method for fluid flows and finite element method to take into account the stresses due to the surface dilational and shear viscosities and surface tension. Validation of the numerical scheme with respect to previous analytic and computational work is provided, with particular attention to the viscosity contrast and the shear and dilational viscosities characterized both by a Boussinesq number$B_{q}$. Then, influence of equal surface viscosities on steady-state characteristics of a droplet in shear flow are studied, considering both small and large deformations and for a large range of bulk viscosity contrast. We find that small deformation analysis is surprisingly predictive at moderate and high surface viscosities. Equal surface viscosities decrease the Taylor deformation parameter and tank-treading angle and also strongly modify the dynamics of the droplet: when the Boussinesq number (surface viscosity) is large relative to the capillary number (surface tension), the droplet displays damped oscillations prior to steady-state tank-treading, reminiscent from the behaviour at large viscosity contrast. In the limit of infinite capillary number$Ca$, such oscillations are permanent. The influence of surface viscosities on breakup is also investigated, and results show that the critical capillary number is increased. A diagram$(B_{q};Ca)$of breakup is established with the same inner and outer bulk viscosities. Additionally, the separate roles of shear and dilational surface viscosity are also elucidated, extending results from small deformation analysis. Indeed, shear (dilational) surface viscosity increases (decreases) the stability of drops to breakup under shear flow. The steady-state deformation (Taylor parameter) varies nonlinearly with each Boussinesq number or a linear combination of both Boussinesq numbers. Finally, the study shows that for certain combinations of shear and dilational viscosities, drop deformation for a given capillary number is the same as in the case of a clean surface while the inclination angle varies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Camenen2016,

title = {Interplay between toroidal rotation and flow shear in turbulence stabilisation},

author = {Y. Camenen and F. J. Casson and P. Manas and A. G. Peeters},

doi = {10.1063/1.4942422},

issn = {1089-7674},

year  = {2016},

date = {2016-02-01},

volume = {23},

number = {2},

publisher = {AIP Publishing},

abstract = {The interplay between toroidal rotation u, parallel flow shear u′, and perpendicular flow shear γE in the stabilisation of tokamak turbulence is investigated in non-linear flux-tube gyrokinetic simulations. The simulations are performed for a reference L-mode DIII-D plasma (the so-called shortfall case) at r/a=0.8, varying the flow parameters around their nominal values. Depending on the respective signs of u, u′, and γE, turbulence is found to be enhanced, reduced, or unchanged. When the coupling is favorable, the overall effect on the non-linear heat fluxes can be very large, even at moderate flow values. The ion heat flux is, for instance, decreased by a factor of 3 when the direction of the parallel flow shear is reversed with respect to its nominal value. Even more surprising, keeping u′ and γE at their nominal values, the ion heat flux decreases by more than 50% when the toroidal flow is reversed. The relevance of this mechanism in the experiments which depends on the ability to decouple u, u′, and γE is discussed. The interplay between u and u′ observed in the non-linear simulations qualitatively follows the linear stability results and is interpreted in the frame of a simple fluid model.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cartier-Michaud2016,

title = {Projection on Proper elements for code control: Verification, numerical convergence, and reduced models. Application to plasma turbulence simulations},

author = {T. Cartier-Michaud and P. Ghendrih and Y. Sarazin and J. Abiteboul and H. Bufferand and G. Dif-Pradalier and X. Garbet and V. Grandgirard and G. Latu and C. Norscini and C. Passeron and P. Tamain},

doi = {10.1063/1.4941974},

issn = {1089-7674},

year  = {2016},

date = {2016-02-01},

volume = {23},

number = {2},

publisher = {AIP Publishing},

abstract = {The Projection on Proper elements (PoPe) is a novel method of code control dedicated to (1) checking the correct implementation of models, (2) determining the convergence of numerical methods, and (3) characterizing the residual errors of any given solution at very low cost. The basic idea is to establish a bijection between a simulation and a set of equations that generate it. Recovering equations is direct and relies on a statistical measure of the weight of the various operators. This method can be used in any number of dimensions and any regime, including chaotic ones. This method also provides a procedure to design reduced models and quantify its ratio of cost to benefit. PoPe is applied to a kinetic and a fluid code of plasma turbulence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Drouot2015b,

title = {Self-generated zonal flows in the plasma turbulence driven by trapped-ion and trapped-electron instabilities},

author = {T. Drouot and E. Gravier and T. Reveille and M. Collard},

doi = {10.1063/1.4933358},

issn = {1089-7674},

year  = {2015},

date = {2015-10-01},

volume = {22},

number = {10},

publisher = {AIP Publishing},

abstract = {This paper presents a study of zonal flows generated by trapped-electron mode and trapped-ion mode micro turbulence as a function of two plasma parameters—banana width and electron temperature. For this purpose, a gyrokinetic code considering only trapped particles is used. First, an analytical equation giving the predicted level of zonal flows is derived from the quasi-neutrality equation of our model, as a function of the density fluctuation levels and the banana widths. Then, the influence of the banana width on the number of zonal flows occurring in the system is studied using the gyrokinetic code. Finally, the impact of the temperature ratio Te/Ti on the reduction of zonal flows is shown and a close link is highlighted between reduction and different gyro-and-bounce-average ion and electron density fluctuation levels. This reduction is found to be due to the amplitudes of gyro-and-bounce-average density perturbations ne and ni gradually becoming closer, which is in agreement with the analytical results given by the quasi-neutrality equation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Drouot2015,

title = {Global gyrokinetic simulations of trapped-electron mode and trapped-ion mode microturbulence},

author = {T. Drouot and E. Gravier and T. Reveille and M. Sarrat and M. Collard and P. Bertrand and T. Cartier-Michaud and P. Ghendrih and Y. Sarazin and X. Garbet},

doi = {10.1063/1.4927920},

issn = {1089-7674},

year  = {2015},

date = {2015-08-01},

volume = {22},

number = {8},

publisher = {AIP Publishing},

abstract = {This paper presents a reduced kinetic model, which describes simultaneously trapped-ion (TIM) and trapped-electron (TEM) driven modes. Interestingly, the model enables the study of a full f problem for ion and electron trapped particles at very low numerical cost. The linear growth rate obtained with the full f nonlinear code Trapped Element REduction in Semi Lagrangian Approach is successfully compared with analytical predictions. Moreover, nonlinear results show some basic properties of collisionless TEM and TIM turbulence in tokamaks. A competition between streamer-like structures and zonal flows is observed for TEM and TIM turbulence. Zonal flows are shown to play an important role in suppressing the nonlinear transport and strongly depend on the temperature ratio Te/Ti.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ghizzo2015,

title = {Shear-flow trapped-ion-mode interaction revisited. I. Influence of low-frequency zonal flow on ion-temperature-gradient driven turbulence},

author = {A. Ghizzo and F. Palermo},

doi = {10.1063/1.4928102},

issn = {1089-7674},

year  = {2015},

date = {2015-08-01},

volume = {22},

number = {8},

publisher = {AIP Publishing},

abstract = {Collisionless trapped ion modes (CTIMs) turbulence exhibits a rich variety of zonal flow physics. The coupling of CTIMs with shear flow driven by the Kelvin-Helmholtz (KH) instability has been investigated. The work explores the parametric excitation of zonal flow modified by wave-particle interactions leading to a new type of resonant low-frequency zonal flow. The KH-CTIM interaction on zonal flow growth and its feedback on turbulence is investigated using semi-Lagrangian gyrokinetic Vlasov simulations based on a Hamiltonian reduction technique, where both fast scales (cyclotron plus bounce motions) are gyro-averaged.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ghizzo2015b,

title = {Shear-flow trapped-ion-mode interaction revisited. II. Intermittent transport associated with low-frequency zonal flow dynamics},

author = {A. Ghizzo and F. Palermo},

doi = {10.1063/1.4928103},

issn = {1089-7674},

year  = {2015},

date = {2015-08-01},

volume = {22},

number = {8},

publisher = {AIP Publishing},

abstract = {We address the mechanisms underlying low-frequency zonal flow generation in turbulent system and the associated intermittent regime of ion-temperature-gradient (ITG) turbulence. This model is in connection with the recent observation of quasi periodic zonal flow oscillation at a frequency close to 2 kHz, at the low-high transition, observed in the ASDEX Upgrade [Conway et al., Phys. Rev. Lett. 106, 065001 (2011)] and EAST tokamak [Xu et al., Phys. Rev. Lett 107, 125001 (2011)]. Turbulent bursts caused by the coupling of Kelvin-Helmholtz (KH) driven shear flows with trapped ion modes (TIMs) were investigated by means of reduced gyrokinetic simulations. It was found that ITG turbulence can be regulated by low-frequency meso-scale zonal flows driven by resonant collisionless trapped ion modes (CTIMs), through parametric-type scattering, a process in competition with the usual KH instability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Favier2015,

title = {Generation and maintenance of bulk turbulence by libration-driven elliptical instability},

author = {B. Favier and A. M. Grannan and M. Le Bars and J. M. Aurnou},

doi = {10.1063/1.4922085},

issn = {1089-7666},

year  = {2015},

date = {2015-06-01},

volume = {27},

number = {6},

publisher = {AIP Publishing},

abstract = {Longitudinal libration corresponds to the periodic oscillation of a body’s rotation rate and is, along with precessional and tidal forcings, a possible source of mechanically-driven turbulence in the fluid interior of satellites and planets. In this study, we present a combination of direct numerical simulations and laboratory experiments, modeling this geophysically relevant mechanical forcing. We investigate the fluid motions inside a longitudinally librating ellipsoidal container filled with an incompressible fluid. The elliptical instability, which is a triadic resonance between two inertial modes and the oscillating base flow with elliptical streamlines, is observed both numerically and experimentally. The large-scale inertial modes eventually lead to small-scale turbulence, provided that the Ekman number is small enough. We characterize this transition to turbulence as additional triadic resonances develop while also investigating the properties of the turbulent flow that displays both intermittent and sustained regimes. These turbulent flows may play an important role in the thermal and magnetic evolution of bodies subject to mechanical forcing, which is not considered in standard models of convectively driven magnetic field generation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fil2015,

title = {Three-dimensional non-linear magnetohydrodynamic modeling of massive gas injection triggered disruptions in JET},

author = {A. Fil and E. Nardon and M. Hoelzl and G. T. A Huijsmans and F. Orain and M. Becoulet and P. Beyer and G. Dif-Pradalier and R. Guirlet and H. R. Koslowski and M. Lehnen and J. Morales and S. Pamela and C. Passeron and C. Reux and F. Saint-Laurent and },

doi = {10.1063/1.4922846},

issn = {1089-7674},

year  = {2015},

date = {2015-06-01},

volume = {22},

number = {6},

publisher = {AIP Publishing},

abstract = {JOREK 3D non-linear MHD simulations of a D2 Massive Gas Injection (MGI) triggered disruption in JET are presented and compared in detail to experimental data. The MGI creates an overdensity that rapidly expands in the direction parallel to the magnetic field. It also causes the growth of magnetic islands (m/n=2/1 and 3/2 mainly) and seeds the 1/1 internal kink mode. O-points of all island chains (including 1/1) are located in front of the MGI, consistently with experimental observations. A burst of MHD activity and a peak in plasma current take place at the same time as in the experiment. However, the magnitude of these two effects is much smaller than in the experiment. The simulated radiation is also much below the experimental level. As a consequence, the thermal quench is not fully reproduced. Directions for progress are identified. Radiation from impurities is a good candidate.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Palermo2015,

title = {Shear flow instabilities induced by trapped ion modes in collisionless temperature gradient turbulence},

author = {F. Palermo and X. Garbet and A. Ghizzo and T. Cartier-Michaud and P. Ghendrih and V. Grandgirard and Y. Sarazin},

doi = {10.1063/1.4916770},

issn = {1089-7674},

year  = {2015},

date = {2015-04-01},

volume = {22},

number = {4},

publisher = {AIP Publishing},

abstract = {One important issue in turbulence self-organization is the interplay between the Kelvin–Helmholtz (KH) instability and streamers and/or zonal flows. This question has been debated for a long time. The effects of the KH instability and its position in the sequence of events between streamers, turbulence, and zonal flows have been investigated with a reduced gyro-bounce averaged kinetic code devoted to study the primary ion temperature gradient (ITG) instability linked to trapped ion modes (TIM). In toroidal geometry, the specific dynamics of TIM linked to trapped particles becomes important when the frequency of ITG modes falls below the ion bounce frequency, allowing one to average on both the cyclotron and bounce motion fast time scales. This reduction of the number of degrees of freedom leads to a strong reduction of computer resources (memory and computation time). Bounce-averaged gyrokinetic code can be considered as a toy model able to describe basic structures of turbulent transport in tokamak devices. In particular, by means of this code, we have observed that the energy injected in the system by the TIM instability is exchanged between streamers and zonal flows by means of KH vortices that grow along these structures in the nonlinear phase. The energy transfer occurs throughout the relaxation phase of the streamer growth leading to a modification of the KH modes and to the generation of the zonal flows.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Poyé2015,

title = {Generation of a magnetic island by edge turbulence in tokamak plasmas},

author = {A. Poyé and O. Agullo and M. Muraglia and X. Garbet and S. Benkadda and A. Sen and N. Dubuit},

doi = {10.1063/1.4916580},

issn = {1089-7674},

year  = {2015},

date = {2015-03-01},

volume = {22},

number = {3},

publisher = {AIP Publishing},

abstract = {We investigate, through extensive 3D magneto-hydro-dynamics numerical simulations, the nonlinear excitation of a large scale magnetic island and its dynamical properties due to the presence of small-scale turbulence. Turbulence is induced by a steep pressure gradient in the edge region [B. D. Scott, Plasma Phys. Controlled Fusion 49, S25 (2007)], close to the separatrix in tokamaks where there is an X-point magnetic configuration. We find that quasi-resonant localized interchange modes at the plasma edge can beat together and produce extended modes that transfer energy to the lowest order resonant surface in an inner stable zone and induce a seed magnetic island. The island width displays high frequency fluctuations that are associated with the fluctuating nature of the energy transfer process from the turbulence, while its mean size is controlled by the magnetic energy content of the turbulence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}