@article{WOS:000896588700001,

title = {On the erosion of cohesive granular soils by a submerged jet: a 

 numerical approach},

author = {Zeyd Benseghier and Li-Hua Luu and Pablo Cuellar and Stephane Bonelli and Pierre Philippe},

doi = {10.1007/s10035-022-01289-5},

issn = {1434-5021},

year  = {2023},

date = {2023-02-01},

journal = {GRANULAR MATTER},

volume = {25},

number = {1},

abstract = {This paper presents an erosion interpretation of cohesive granular 

 materials stressed by an impinging jet based on the results of a 

 micromechanical simulation model. The numerical techniques are briefly 

 described, relying on a two-dimensional Lattice Boltzmann Method coupled 

 with a Discrete Element Methods including a simple model of solid 

 intergranular cohesion. These are then used to perform a parametric 

 study of a planar jet in the laminar regime impinging the surface of 

 granular samples with different degrees of cohesive strength. The 

 results show the pertinence of using a generalized form of the Shields 

 criterion for the quantification of the erosion threshold, which is 

 valid for cohesionless samples, through empirical calibration, and also 

 for cohesive ones. Furthermore, the scouring kinetics are analysed here 

 from the perspective of a self-similar expansion of the eroded crater 

 leading to the identification of a characteristic erosion time and the 

 quantification of the classical erosion coefficient. However, the 

 presented results also challenge the postulate of a local erosion law 

 including erodibility parameters as intrinsic material properties. The 

 paper then reviews the main limitations of the simulation and current 

 interpretation models, and discusses the potential causes for the 

 observed discrepancies, questioning the pertinence of using 

 time-averaged macroscopic relations to correctly describe soil erosion. 

 The paper concludes addressing this question with a complementary study 

 of the presented simulations re-assessed at the particle-scale. The 

 resulting local critical shear stress of single grains reveals a very 

 wide dispersion of the data but nevertheless appears to confirm the 

 general macroscopic trend derived for the cohesionless samples, while 

 the introduction of cohesion implies a significant but systematic 

 quantitative deviation between the microscopic and macroscopic 

 estimates. Nevertheless, the micro data still shows consistently that 

 the critical shear stress does actually vary approximately in linear 

 proportion of the adhesive force.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lemasquerier_2023,

title = {Zonal jets experiments in the gas giants' zonostrophic regime},

author = {D. Lemasquerier and B. Favier and M. Le Bars},

url = {https://doi.org/10.1016%2Fj.icarus.2022.115292},

doi = {10.1016/j.icarus.2022.115292},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Icarus},

volume = {390},

pages = {115292},

publisher = {Elsevier BV},

abstract = {Intense east-west winds called zonal jets are observed in the atmospheres of Jupiter and Saturn and extend in their deep interior. We present experimental results from a fully three-dimensional laboratory analog of deep gas giants zonal jets. We use a rapidly rotating deep cylindrical tank, filled with water, and forced by a small-scale hydraulic circulation at the bottom. A topographic β-effect is naturally present because of the curvature of the free surface. Instantaneous turbulent zonal jets spontaneously emerge from the small-scale forcing, equilibrate at large scale, and can contain up to 70% of the total kinetic energy of the flow once in a quasi-steady state. We show that the spectral properties of the experimental flows are consistent with the theoretical predictions in the zonostrophic turbulence regime, argued to be relevant to gas giants. This constitutes the first fully-experimental validation of the zonostrophic theory in a completely three-dimensional framework. Complementary, quasi-geostrophic (QG) simulations show that this result is not sensitive to the forcing scale. Next, we quantify the potential vorticity (PV) mixing. While PV staircasing should emerge in the asymptotic regime of the gas giants, only a moderate PV mixing occurs because of the strong forcing and dissipation, as confirmed by QG simulations at smaller Ekman number. We quantify the local PV mixing by measuring the equivalent of a Thorpe scale, and confirm that it can be used to estimate the upscale energy transfer rate of the flow, which otherwise needs to be estimated from a much more demanding spectral analysis. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000860284900009,

title = {Breakups of Chitosan microcapsules in extensional flow},

author = {Revaz Chachanidze and Kaili Xie and Jinming Lyu and Marc Jaeger and Marc Leonetti},

doi = {10.1016/j.jcis.2022.08.169},

issn = {0021-9797},

year  = {2023},

date = {2023-01-01},

journal = {JOURNAL OF COLLOID AND INTERFACE SCIENCE},

volume = {629},

number = {A},

pages = {445-454},

abstract = {The controlled rupture of a core-shell capsule and the timely release of 

 encapsulated materials are essential steps of the efficient design of 

 such carriers. The mechanical and physico-chemical properties of their 

 shells (or membranes) mainly govern the evolution of such systems under 

 stress and notably the link between the dynamics of rupture and the 

 mechanical properties. This issue is addressed considering weakly 

 cohesive shells made by the interfacial complexation of Chitosan and 

 PFacid in a planar extensional flow. Three regimes are observed, thanks 

 to the two observational planes. Whatever the time of reaction in 

 membrane assembly, there is no rupture in deformation as long as the 

 hydrodynamic stress is below a critical value. At low times of 

 complexation (weak shear elastic modulus), the rupture is reminiscent of 

 the breakup of dro-plets: a dumbell or a waist. Fluorescent labelling of 

 the membrane shows that this process is governed by continuous thinning 

 of the membrane up to the destabilization. It is likely that the 

 membrane shows a tran-sition from a solid to liquid state. At longer 

 times of complexation, the rupture has a feature of solid-like breakup 

 (breakage) with a discontinuity of the membrane. The maximal internal 

 constraint determined numerically marks the initial location of breakup 

 as shown. The pattern becomes more complex as the elon-gation rate 

 increases with several points of rupture. A phase diagram in the space 

 parameters of the shear elastic modulus and the hydrodynamic stress is 

 established.(c) 2022 Elsevier Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000909958900001,

title = {Investigation of PbSnTeSe High-Entropy Thermoelectric Alloy: A DFT 

 Approach},

author = {Ming Xia and Marie-Christine Record and Pascal Boulet},

doi = {10.3390/ma16010235},

year  = {2023},

date = {2023-01-01},

journal = {MATERIALS},

volume = {16},

number = {1},

abstract = {Thermoelectric materials have attracted extensive attention because they 

 can directly convert waste heat into electric energy. As a brand-new 

 method of alloying, high-entropy alloys (HEAs) have attracted much 

 attention in the fields of materials science and engineering. Recent 

 researches have found that HEAs could be potentially good thermoelectric 

 (TE) materials. In this study, special quasi-random structures (SQS) of 

 PbSnTeSe high-entropy alloys consisting of 64 atoms have been generated. 

 The thermoelectric transport properties of the highest-entropy 

 PbSnTeSe-optimized structure were investigated by combining calculations 

 from first-principles density-functional theory and on-the-fly machine 

 learning with the semiclassical Boltzmann transport theory and 

 Green-Kubo theory. The results demonstrate that PbSnTeSe HEA has a very 

 low lattice thermal conductivity. The electrical conductivity, thermal 

 electronic conductivity and Seebeck coefficient have been evaluated for 

 both n-type and p-type doping. N-type PbSnTeSe exhibits better power factor (PF = S-2 sigma) than p-type PbSnTeSe because of larger 

 electrical conductivity for n-type doping. Despite high electrical 

 thermal conductivities, the calculated ZT are satisfactory. The maximum 

 ZT (about 1.1) is found at 500 K for n-type doping. These results 

 confirm that PbSnTeSe HEA is a promising thermoelectric material.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000893459000001,

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

author = {Gregoire David and Nicolas Ferre and Boris Le Guennic},

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

issn = {1549-9618},

year  = {2022},

date = {2022-12-31},

journal = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},

abstract = {The use of broken-symmetry calculations in Kohn- Sham density functional 

 theory has offered an affordable route to study magnetic exchange 

 couplings in transition-metal-based compounds. However, computing this 

 property in compounds exhibiting several couplings is still challenging 

 and especially due to the difficulties to overcome the well-known 

 problem of spin contamination. Here, we present a new and general method 

 to compute magnetic exchange couplings in systems featuring several spin 

 sites. To provide a consistent spin decontamination of J values, our 

 strategy exploits the decomposition method of the magnetic exchange 

 coupling proposed by Coulaud et al. and generalizes our previous work on 

 diradical compounds where the overall magnetic exchange coupling is 

 defined as the sum of its three main and properly extracted physical 

 contributions (direct exchange, kinetic exchange, and spin 

 polarization). In this aim, the generalized extraction of all 

 contributions is presented to systems with multiple spin sites bearing 

 one unpaired electron. This is done by proposing a new paradigm to treat 

 the kinetic exchange contribution, which proceeds through 

 monorelaxations of the magnetic orbitals. This method, so-called the 

 recomposition method, is applied to a compound featuring three Cu(II) 

 ions with a linear arrangement and to a recently synthesized complex 

 containing a Cu4O4 cubane unit presenting an unusual magnetic behavior.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000906466000001,

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 Ferre and Seunghoon Lee and Cheol Ho Choi},

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

issn = {1549-9618},

year  = {2022},

date = {2022-12-31},

journal = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},

abstract = {The photochemistry of nucleobases, important for their role as building 

 blocks of DNA, is largely affected by the electrostatic environment in 

 which they are soaked. For example, despite the numerous studies of 

 thymine in solution and DNA, there is still a debate on the 

 photochemical deactivation pathways after UV absorption. Many 

 theoretical models are oversimplified due to the lack of computationally 

 accurate and efficient electronic structure methodologies that capture 

 excited state electron correlation effects when nucleobases are embedded 

 in large electrostatic media. Here, we combine mixed-reference spin-flip 

 time-dependent density functional theory (MRSF-TDDFT) with electrostatic 

 embedding QM/MM using electrostatic potential fittingfitted (ESPF) 

 atomic charges, as a strategy to accurately and efficiently describe the 

 electronic structure of chromophores polarized by an electrostatic 

 medium. In particular, we develop analytic expressions for the energy 

 and gradient of MRSF/MM based on the ESPF coupling using atom-centered 

 grids and total charge conservation. We apply this methodology to the 

 study of solvation effects on thymine photochemistry in water and 

 thymine dimers in DNA. In the former, the combination of trajectory 

 surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with 

 MRSF/MM remarkably revealed accelerated deactivation decay pathways, 

 which is consistent with the experimental decay time of similar to 400 

 fs. The enhanced hopping rate can be explained by the preferential 

 stabilization of corresponding conical interactions due to their 

 increased dipole moments. Structurally, it is a consequence of 

 characteristic methyl puckered geometries near the conical intersection 

 region. For the thymine dimer in B-DNA, we found new photochemical 

 pathways through conical intersections that could explain the formation 

 of cyclobutadiene dimers and 6-4 photoproducts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000892955400001,

title = {Spontaneous suppression of inverse energy cascade in instability-driven 

 2-D turbulence},

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

doi = {10.1017/jfm.2022.935},

issn = {0022-1120},

year  = {2022},

date = {2022-12-01},

journal = {JOURNAL OF FLUID MECHANICS},

volume = {952},

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{WOS:000897848100001,

title = {Localized compressional self-heating in magnetic islands},

author = {Daniele Villa and Nicolas Dubuit and Olivier Agullo and Alexandre Poye and Xavier Garbet and Andrei Smolyakov},

doi = {10.1017/S0022377822001234},

issn = {0022-3778},

year  = {2022},

date = {2022-12-01},

journal = {JOURNAL OF PLASMA PHYSICS},

volume = {88},

number = {6},

abstract = {A spontaneous heating process is found to arise in a system where a 

 magnetic island is present due to a linearly unstable tearing mode. The 

 parity, the relative phases and the structure of the fields determined 

 linearly by the tearing mode cause the compression of the plasma in the 

 direction parallel to the magnetic field to heat the plasma in the 

 vicinity of the separatrix in the nonlinear phase. Using a six-field 

 electromagnetic fluid model, the process is found to be present in both 

 two-dimensional single-helicity and three-dimensional multi-helicity 

 simulations with both symmetric and asymmetric magnetic equilibrium 

 profiles. A noteworthy feature of the model is that the higher-order 

 compression terms responsible for the heating process are retained in 

 the equations. The process is believed to be linked to experimental 

 observations of localized hot-spots on externally induced magnetic 

 islands.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000828406700001,

title = {Atomistic investigation on the impact of substitutional Al and Si atoms 

 on the carbon kinetics in ferrite},

author = {Liangzhao Huang and Paul Eymeoud and Philippe Maugis},

doi = {10.1016/j.jallcom.2022.166031},

issn = {0925-8388},

year  = {2022},

date = {2022-11-01},

journal = {JOURNAL OF ALLOYS AND COMPOUNDS},

volume = {921},

abstract = {The pairwise interactions of substitutional solute atom X = Al, Si with 

 interstitial carbon at stable (octa-hedral) and saddle-point 

 (tetrahedral) positions in body-centered-cubic iron (alpha-Fe) are 

 computed using density-functional theory. These pairwise interactions 

 are used in atomistic kinetic Monte Carlo approach to simulate carbon 

 internal friction and tracer diffusion measurements in Fe-Si, Fe-Al, and 

 Fe-Al-Si ferritic alloys without any adjusting parameters. The good 

 agreement between the simulated and experimental Snoek relaxation 

 profiles validates the pair interaction model for kinetic simulations. 

 The predicted effect of Al on slowing down carbon diffusion is 

 consistent with previous studies. We highlight a super-cell size effect 

 on the Si-carbon interactions obtained from first principles. Using a 

 carefully tested database, it is shown that the introduction of Si into 

 ferrite only decreases the carbon diffusivity below a critical 

 tem-perature.(c) 2022 Elsevier B.V. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000861453100010,

title = {Lattice-Boltzmann modeling of lifted hydrogen jet flames: A new model 

 for hazardous ignition prediction},

author = {Said Taileb and Alejandro Millan-Merino and Song Zhao and Pierre Boivin},

doi = {10.1016/j.combustflame.2022.112317},

issn = {0010-2180},

year  = {2022},

date = {2022-11-01},

journal = {COMBUSTION AND FLAME},

volume = {245},

abstract = {This numerical study deals with the hazardous ignition of a jet flame in 

 a vitiated co-flow. A novel formulation, based on a passive scalar 

 variable, will be presented to predict hydrogen auto-ignition events. 

 The model, derived from the theoretical analysis of the Jacobian, 

 correctly describes the appearance and absence of auto-ignition in 

 complex configurations based on initial thermodynamic and mixture 

 conditions. No chemical reaction and species equations are required to 

 perform the simulations. Results of Lattice Boltzmann Methods (LBM) 

 simulations of a 3D H-2/N-2 Cabra flame will be presented using a 

 detailed H-2-Air mechanism. Validation against experimental and 

 numerical results will be provided for the lift-off (distance to 

 auto-ignition). The passive scalar predictions are successfully compared 

 with the reactive simulations. The results show a potential extension of 

 this model to an extensive spectrum of hydrogen safety and large-scale 

 turbulent combustion applications. (C) 2022 The Combustion Institute. 

 Published by Elsevier Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000829352300004,

title = {Numerical model for sessile drop evaporation on heated substrate under 

 microgravity},

author = {Sanjeev Kumar and Marc Medale and David Brutin},

doi = {10.1016/j.ijheatmasstransfer.2022.123150},

issn = {0017-9310},

year  = {2022},

date = {2022-10-01},

journal = {INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER},

volume = {195},

abstract = {Although sessile drops have simple geometries, the physics involved in 

 their evaporation process is com-plex owing to their numerous intricate 

 interactions and their fluid nature. An accurate quantitative model of 

 the evaporation process will enable increased understanding and control 

 over the process. In this study, a numerical model is developed for 

 sessile drop evaporation on a heated substrate under microgravity based 

 on the results of rocket and parabolic experiments to understand the 

 `internal dynamics of a ses-sile drop. The model is quantitatively 

 validated through experiments. Subsequently, a correlation between 

 substrate temperature and evaporation rate is suggested for an ethanol 

 sessile drop. The flow motion is analyzed by conducting 

 three-dimensional resolved computations of an evaporating sessile drop. 

 This provides insights into the Marangoni effect in the dynamics of the 

 evaporation process and the occur-rence of secondary instabilities. For 

 the first time, the fine effects of secondary instabilities on the 

 evap-oration rate are captured. Our numerical model is valid in the 

 absence of convection in the vapor phase, producing an interface of an 

 evaporating drop in a fully saturated vapor, which typically exists 

 under microgravity conditions. (c) 2022 Elsevier Ltd. All rights 

 reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000885378200003,

title = {Non-Kasha fluorescence of pyrene emerges from a dynamic equilibrium 

 between excited states},

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

doi = {10.1063/5.0113908},

issn = {0021-9606},

year  = {2022},

date = {2022-10-01},

journal = {JOURNAL OF CHEMICAL PHYSICS},

volume = {157},

number = {15},

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 (S-2) 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 S-2 

 emission. We show that the non-Kasha behavior is a dynamic-equilibrium 

 effect not caused by a metastable S-2 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 S-2 emission was not observed in some 

 experiments. (C) 2022 Author(s).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000867091700011,

title = {Morphology and dynamical stability of self-gravitating vortices 

 Numerical simulations},

author = {S. Rendon Restrepo and P. Barge},

doi = {10.1051/0004-6361/202243518},

issn = {0004-6361},

year  = {2022},

date = {2022-10-01},

journal = {ASTRONOMY & ASTROPHYSICS},

volume = {666},

abstract = {Context. Theoretical and numerical studies have shown that large-scale 

 vortices in protoplanetary discs can result from various hydro-dynamical 

 instabilities. Once produced, such vortices can survive nearly unchanged 

 over a large number of rotation periods, slowly migrating towards the 

 star. Lopsided asymmetries recently observed at sub-millimetre and 

 millimetre wavelengths in a number of transition discs could be 

 explained by the emission of the solid particles trapped by vortices in 

 the outer disc. However, at such a distance from the star, disc 

 self-gravity (SG) may affect the vortex evolution and must be included 

 in models. 

 Aims. Our first goal is to identify how vortex morphology is affected by 

 its own gravity. Next, we look for conditions that a self-gravitating 

 disc must satisfy in order to permit vortex survival at long timescales. 

 Finally, we characterise as well as possible the persistent 

 self-gravitating vortices we have found in isothermal and non-isothermal 

 discs. 

 Methods. We performed 2D hydrodynamic simulations using the RoSSBi 3.0 

 code. The outline of our computations was limited to Euler's equations 

 assuming a non-homentropic and non-adiabatic flow for an ideal gas. A 

 series of 45 runs were carried out starting from a Gaussian 

 vortex-model; the evolution of vortices was followed during 300 orbits 

 for various values of the vortex parameters and the Toomre parameter. 

 Two simulations, with the highest resolution thus far for studies of 

 vortices, were also run to better characterise the internal structure of 

 the vortices and for the purpose of comparison with an isothermal case. 

 Results. We find that SG tends to destabilise the injected vortices, but 

 compact small-scale vortices seem to be more robust than large-scale 

 oblong vortices. Vortex survival critically depends on the value of the 

 disc's Toomre parameter, but may also depend on the disc temperature at 

 equilibrium. Disc SG must be small enough to avoid destruction in 

 successive splitting and an approximate `stability' criterion is deduced 

 for vortices. The self-gravitating vortices that we found persist during 

 hundreds of rotation periods and look like the quasi-steady vortices 

 obtained in the non-self-gravitating case. A number of these 

 self-gravitating vortices are eventually accompanied by a secondary 

 vortex with a horseshoe motion. These vortices reach a new rotational 

 equilibrium in their core, tend to contract in the radial direction, and 

 spin faster. 

 Conclusions. We propose an approximate `robustness criterion', which 

 states that, for a given morphology, a vortex appears stable provided 

 that the disc's Toomre parameter overcomes a fixed threshold. Global 

 simulations with a high enough numerical resolution are required to 

 avoid inappropriate decay and to follow the evolution of 

 self-gravitating vortices in protoplanetary discs. Vortices reach a 

 nearly steady-state more easily in non-isothermal discs than in 

 isothermal discs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000876981400001,

title = {Direct structural observation of ultrafast photoisomerization dynamics 

 in sinapate esters},

author = {Temitope T. Abiola and Josene M. Toldo and Mariana T. Casal and Amandine L. Flourat and Benjamin Rioux and Jack M. Woolley and Daniel Murdock and Florent Allais and Mario Barbatti and Vasilios G. Stavros},

doi = {10.1038/s42004-022-00757-6},

issn = {2399-3669},

year  = {2022},

date = {2022-10-01},

journal = {COMMUNICATIONS CHEMISTRY},

volume = {5},

number = {1},

abstract = {Sinapate esters have been extensively studied for their potential 

 application in `nature-inspired' photoprotection. There is general 

 consensus that the relaxation mechanism of sinapate esters following 

 photoexcitation with ultraviolet radiation is mediated by geometric 

 isomerization. This has been largely inferred through indirect studies 

 involving transient electronic absorption spectroscopy in conjunction 

 with steady-state spectroscopies. However, to-date, there is no direct 

 experimental evidence tracking the formation of the photoisomer in 

 real-time. Using transient vibrational absorption spectroscopy, we 

 report on the direct structural changes that occur upon photoexcitation, 

 resulting in the photoisomer formation. Our mechanistic analysis 

 predicts that, from the photoprepared pi pi* state, internal 

 conversion takes place through a conical intersection (CI) near the 

 geometry of the initial isomer. Our calculations suggest that different 

 CI topographies at relevant points on the seam of intersection may 

 influence the isomerization yield. Altogether, we provide compelling 

 evidence suggesting that a sinapate ester's geometric isomerization can 

 be a more complex dynamical process than originally thought. 

 Photoinduced isomerization reactions can be used to efficiently 

 dissipate absorbed energy in photosystems such as molecular motors, but 

 the ultrafast processes are challenging to characterize. Here, the 

 authors track the formation of the E and Z isomers of ethyl sinapate in 

 real time via transient vibrational absorption spectroscopy and find 

 that photoinduced internal conversion occurs at multiple points along 

 the potential energy surface.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000868782300001,

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 = {1070-664X},

year  = {2022},

date = {2022-10-01},

journal = {PHYSICS OF PLASMAS},

volume = {29},

number = {10},

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. Published under an exclusive license by AIP Publishing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000859790500001,

title = {Using diketopyrrolopyrroles to stabilize double excitation and control 

 internal conversion},

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

doi = {10.1039/d2cp03533b},

issn = {1463-9076},

year  = {2022},

date = {2022-10-01},

journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},

volume = {24},

number = {38},

pages = {23279-23288},

abstract = {Diketopyrrolopyrrole (DPP) is a pivotal functional group to tune the 

 physicochemical properties of novel organic photoelectronic materials. 

 Among multiple uses, DPP-thiophene derivatives forming a dimer through a 

 vinyl linker were recently shown to quench the fluorescence observed in 

 their isolated monomers. Here, we explain this fluorescence quenching 

 using computational chemistry. The DPP-thiophene dimer has a low-lying 

 doubly excited state that is not energetically accessible for the 

 monomer. This state delays the fluorescence allowing internal conversion 

 to occur first. We characterize the doubly excited state wavefunction by 

 systematically changing the derivatives to tune the pi-scaffold size and 

 the acceptor and donor characters. The origin of this state's 

 stabilization is related to the increase in the pi-system and not to the 

 charge-transfer features. This analysis delivers core conceptual 

 information on the electronic properties of organic chromophores 

 arranged symmetrically around a vinyl linker, opening new ways to 

 control the balance between luminescence and internal conversion.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000814754000002,

title = {Group-level inference of information-based measures for the analyses of 

 cognitive brain networks from neurophysiological data},

author = {Etienne Combrisson and Michele Allegra and Ruggero Basanisi and Robin A. A. Ince and Bruno L. Giordano and Julien Bastin and Andrea Brovelli},

doi = {10.1016/j.neuroimage.2022.119347},

issn = {1053-8119},

year  = {2022},

date = {2022-09-01},

journal = {NEUROIMAGE},

volume = {258},

abstract = {The reproducibility crisis in neuroimaging and in particular in the case 

 of underpowered studies has introduced doubts on our ability to 

 reproduce, replicate and generalize findings. As a response, we have 

 seen the emergence of suggested guidelines and principles for 

 neuroscientists known as Good Scientific Practice for conducting more 

 reliable research. Still, every study remains almost unique in its 

 combination of analytical and statistical approaches. While it is 

 understandable considering the diversity of designs and brain data 

 recording, it also represents a striking point against reproducibility. 

 Here, we propose a non-parametric permutation-based statistical 

 framework, primarily designed for neurophysiological data, in order to 

 perform group-level inferences on non negative measures of information 

 encompassing metrics from information-theory, machine-learning or 

 measures of distances. The framework supports both fixed-and 

 random-effect models to adapt to inter-individuals and inter-sessions 

 variability. Using numerical simulations, we compared the accuracy in 

 ground-truth retrieving of both group models, such as test-and 

 cluster-wise corrections for multiple comparisons. We then reproduced 

 and extended existing results using both spatially uniform MEG and 

 non-uniform intracranial neurophysiological data. We showed how the 

 framework can be used to extract stereotypical task-and behavior-related 

 effects across the population covering scales from the local level of 

 brain regions, inter-areal functional connectivity to measures 

 summarizing network properties. We also present an open-source Python 

 toolbox called Frites1 that includes the proposed statistical pipeline 

 using information-theoretic metrics such as single-trial functional 

 connectivity estimations for the extraction of cognitive brain networks. 

 Taken together, we believe that this framework deserves careful 

 attention as its robustness and flexibility could be the starting point 

 toward the uniformization of statistical approaches.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000850173400001,

title = {Accurate computed singlet-triplet energy differences for cobalt systems: 

 implication for two-state reactivity},

author = {Leo Chaussy and Denis Hagebaum-Reignier and Stephane Humbel and Paola Nava},

doi = {10.1039/d2cp03291k},

issn = {1463-9076},

year  = {2022},

date = {2022-09-01},

journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},

volume = {24},

number = {36},

pages = {21841-21852},

abstract = {Accurate singlet-triplet energy differences for cobalt and rhodium 

 complexes were calculated by using several wave function methods, such 

 as MRCISD, CASPT2, CCSD(T) and BCCD(T). Relaxed energy differences were 

 obtained by considering the singlet and triplet complexes, each at the 

 minimum of their potential energy surfaces. Active spaces for 

 multireference calculations were carefully checked to provide accurate 

 results. The considered systems are built by increasing progressively 

 the first coordination sphere around the metal. We included in our set two CpCoX complexes (Cp = cyclopentadienyl},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000874281500001,

title = {Application of immersed boundary based turbulence wall modeling to the 

 Ahmed body aerodynamics},

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

doi = {10.1063/5.0098232},

issn = {1070-6631},

year  = {2022},

date = {2022-09-01},

journal = {PHYSICS OF FLUIDS},

volume = {34},

number = {9},

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 degrees 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. Published under an exclusive license by AIP 

 Publishing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000842506600001,

title = {Competition between Rayleigh-Benard and horizontal convection},

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

doi = {10.1017/jfm.2022.613},

issn = {0022-1120},

year  = {2022},

date = {2022-08-01},

journal = {JOURNAL OF FLUID MECHANICS},

volume = {947},

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) <= Ra-F <= 

 10(9) and imposed top horizontal to bottom vertical heat flux ratios 0 <= Lambda <= 1. The fluid domain is a closed two-dimensional box with aspect ratio 4 <= Gamma <= 16 and we consider no-slip boundaries and 

 adiabatic side walls. We demonstrate a regime transition from 

 Rayleigh-Bdnard (RB) convection to HC at Lambda approximate to 10(-2), 

 which is independent of Ra-F and Gamma. At small Lambda, the flow is 

 organised in multiple overturning cells with approximately unit aspect 

 ratio, whereas at large Lambda 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-F Lambda 

 Gamma(4) are in good agreement with previous results from classical RB 

 convection and HC studies in the limit Lambda << 10(-2) and Lambda >> 

 10(-2), respectively. We demonstrate that the system is multi-stable 

 near the transition Lambda approximate to 10(-2), i.e. the exact number 

 of cells not only depends on Lambda 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{WOS:000842613300001,

title = {Probing the electronic structure and photophysics of 

 thiophene-diketopyrrolopyrrole derivatives in solution},

author = {Daniel W. Polak and Mariana T. 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 = {1463-9076},

year  = {2022},

date = {2022-08-01},

journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},

volume = {24},

number = {34},

pages = {20138-20151},

abstract = {Diketopyrrolopyrroles are a popular class of electron-withdrawing unit 

 in optoelectronic materials. When combined with electron donating 

 side-chain functional groups such as thiophenes, they form a very broad 

 class of donor-acceptor molecules: thiophene-diketopyrrolopyrroles 

 (TDPPs). Despite their widescale use in biosensors and photovoltaic 

 materials, studies have yet to establish the important link between the 

 electronic structure of the specific TDPP and the critical optical 

 properties. To bridge this gap, ultrafast transient absorption with 22 

 fs time resolution has been used to explore the photophysics of three 

 prototypical TDPP molecules: a monomer, dimer and polymer in solution. 

 Interpretation of experimental data was assisted by a recent high-level 

 theoretical study, and additional density functional theory 

 calculations. These studies show that the photophysics of these 

 molecular prototypes under visible photoexcitation are determined by 

 just two excited electronic states, having very different electronic 

 characters (one is optically bright, the other dark), their relative 

 energetic ordering and the timescales for internal conversion from one 

 to the other and/or to the ground state. The underlying difference in 

 electronic structure alters the branching between these excited states 

 and their associated dynamics. In turn, these factors dictate the 

 fluorescence quantum yields, which are shown to vary by similar to 1-2 

 orders of magnitude across the TDPP prototypes investigated here. The 

 fast non-radiative transfer of molecules from the bright to dark states 

 is mediated by conical intersections. Remarkably, wavepacket signals in 

 the measured transient absorption data carry signatures of the nuclear 

 motions that enable mixing of the electronic-nuclear wavefunction and 

 facilitate non-adiabatic coupling between the bright and dark states.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000842613300001b,

title = {Probing the electronic structure and photophysics of 

 thiophene-diketopyrrolopyrrole derivatives in solution},

author = {Daniel W. Polak and Mariana T. 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 = {1463-9076},

year  = {2022},

date = {2022-08-01},

journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},

volume = {24},

number = {34},

pages = {20138-20151},

abstract = {Diketopyrrolopyrroles are a popular class of electron-withdrawing unit 

 in optoelectronic materials. When combined with electron donating 

 side-chain functional groups such as thiophenes, they form a very broad 

 class of donor-acceptor molecules: thiophene-diketopyrrolopyrroles 

 (TDPPs). Despite their widescale use in biosensors and photovoltaic 

 materials, studies have yet to establish the important link between the 

 electronic structure of the specific TDPP and the critical optical 

 properties. To bridge this gap, ultrafast transient absorption with 22 

 fs time resolution has been used to explore the photophysics of three 

 prototypical TDPP molecules: a monomer, dimer and polymer in solution. 

 Interpretation of experimental data was assisted by a recent high-level 

 theoretical study, and additional density functional theory 

 calculations. These studies show that the photophysics of these 

 molecular prototypes under visible photoexcitation are determined by 

 just two excited electronic states, having very different electronic 

 characters (one is optically bright, the other dark), their relative 

 energetic ordering and the timescales for internal conversion from one 

 to the other and/or to the ground state. The underlying difference in 

 electronic structure alters the branching between these excited states 

 and their associated dynamics. In turn, these factors dictate the 

 fluorescence quantum yields, which are shown to vary by similar to 1-2 

 orders of magnitude across the TDPP prototypes investigated here. The 

 fast non-radiative transfer of molecules from the bright to dark states 

 is mediated by conical intersections. Remarkably, wavepacket signals in 

 the measured transient absorption data carry signatures of the nuclear 

 motions that enable mixing of the electronic-nuclear wavefunction and 

 facilitate non-adiabatic coupling between the bright and dark states.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000819454900001,

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 = {1549-9618},

year  = {2022},

date = {2022-07-08},

journal = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},

abstract = {The problem associated with the zero-point energy (ZPE) leak in 

 classical trajectory calculations is well known. Since ZPE is a 

 manifestation of the quantum uncertainty principle, there are no 

 restrictions on energy during the classical propagation of nuclei. This 

 phenomenon can lead to unphysical results, such as forming products 

 without the ZPE in the internal vibrational degrees of freedom (DOFs). 

 The ZPE leakage also permits reactions below the quantum threshold for 

 the reaction. We have developed a new Hessian-free method, inspired by 

 the LoweAndersen thermostat model, to prevent energy dipping below a 

 threshold in the localpair (LP) vibrational DOFs. The idea is to pump 

 the leaked energy to the corresponding local vibrational mode taken from 

 the other vibrational DOFs. We have applied the new correction protocol 

 on the ab-initio ground-state molecular dynamics simulation of the water 

 dimer (H2O)2, which dissociates due to unphysical ZPE spilling from 

 high-frequency OH modes. The LP-ZPE method has been able to prevent the 

 ZPE spilling of the OH stretching modes by pumping back the leaked 

 energy into the corresponding modes, while this energy is taken from the 

 other modes of the dimer itself, keeping the system as a microcanonical 

 ensemble.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000831554100012,

title = {Viral infection engenders bona fide and bystander subsets of 

 lung-resident memory B cells through a permissive mechanism},

author = {Claude Gregoire and Lionel Spinelli and Sergio Villazala-Merino and Laurine Gil and Maria Pia Holgado and Myriam Moussa and Chuang Dong and Ana Zarubica and Mathieu Fallet and Jean-Marc Navarro and Bernard Malissen and Pierre Milpied and Mauro Gaya},

doi = {10.1016/j.immuni.2022.06.002},

issn = {1074-7613},

year  = {2022},

date = {2022-07-01},

journal = {IMMUNITY},

volume = {55},

number = {7},

pages = {1216+},

abstract = {Lung-resident memory B cells (MBCs) provide localized protection against 

 reinfection in respiratory airways. Currently, the biology of these 

 cells remains largely unexplored. Here, we combined influenza and 

 SARS-CoV-2 infection with fluorescent-reporter mice to identify MBCs 

 regardless of antigen specificity. We found that two main 

 transcriptionally distinct subsets of MBCs colonized the lung 

 peribronchial niche after infec-tion. These subsets arose from different 

 progenitors and were both class switched, somatically mutated, and 

 intrinsically biased in their differentiation fate toward plasma cells. 

 Combined analysis of antigen spec-ificity and B cell receptor repertoire 

 segregated these subsets into ???bona fide???virus-specific MBCs and 

 ???bystander???MBCs with no apparent specificity for eliciting viruses 

 generated through an alternative permis-sive process. Thus, diverse 

 transcriptional programs in MBCs are not linked to specific effector 

 fates but rather to divergent strategies of the immune system to 

 simultaneously provide rapid protection from reinfec-tion while 

 diversifying the initial B cell repertoire.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000806828200002,

title = {Carbon diffusion in bcc- and bct-Fe: Influence of short-range C-C pair 

 interactions studied from first-principles calculations},

author = {Dmytro Kandaskalov and Liangzhao Huang and Johnathan Emo and Philippe Maugis},

doi = {10.1016/j.matchemphys.2022.126159},

issn = {0254-0584},

year  = {2022},

date = {2022-07-01},

journal = {MATERIALS CHEMISTRY AND PHYSICS},

volume = {286},

abstract = {Identifying the mechanisms of interstitial diffusion in iron is 

 important to understanding the low-temperature ageing of Fe-C ferritic 

 and martensitic alloys. In spite of the low solubility of carbon in 

 ferrite at equilibrium, carbon-rich areas are often found at segregated 

 grain boundaries and in Cottrell atmospheres around dislo-cations. 

 Carbon-rich areas also form by spinodal decomposition in martensite. In 

 those cases, carbon atoms experience short-range interactions, 

 susceptible to modify their migration behaviour. We performed 

 first-principles calculations to study the influence of these C-C 

 interactions on the migration of interstitial carbon in body -centered 

 iron. The ab initio energy database was introduced in kinetic Monte 

 Carlo simulations to compute the thermodynamic and kinetic parameters. 

 We found that the migration energies of carbon are largely affected by 

 the presence of a neighbouring carbon atom. We explain the evolution of 

 these energies by the relative stability of the C-C configurations 

 corresponding to stable and transition-state positions. The C-C pair 

 interactions slightly modify the ferrite/martensite transition 

 conditions and significantly change the carbon atomic migration path. 

 The latter leads to an increase of the diffusivity up to 10 times and an 

 important kinetic correlation at low temperature (< 300 K) and high 

 carbon contents (> 1 at.%).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000770897700001,

title = {A Lattice-Boltzmann study of premixed flames thermo-acoustic 

 instabilities},

author = {Karthik Bhairapurada and Bruno Denet and Pierre Boivin},

doi = {10.1016/j.combustflame.2022.112049},

issn = {0010-2180},

year  = {2022},

date = {2022-06-01},

journal = {COMBUSTION AND FLAME},

volume = {240},

abstract = {We present possibly for the first time Lattice-Boltzmann numerical 

 simulations of thermo-acoustic instabilities of premixed flames. We 

 study flames interacting with an imposed acoustic field where flames 

 submitted to a parametric instability can be observed, as well as plane 

 flames re-stabilized by the acoustic forcing. Self-induced 

 thermo-acoustic oscillations of flames propagating in narrow channels 

 are also studied, indicating an unexpected dependency with the channel 

 width. For both excited and self-excited flames, results confirm that 

 Lattice-Boltzmann method can capture the complex coupling between flame 

 dynamics and acoustics.(c) 2022 The Combustion Institute. Published by 

 Elsevier Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000804941300001,

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 = {1070-6631},

year  = {2022},

date = {2022-05-01},

journal = {PHYSICS OF FLUIDS},

volume = {34},

number = {5},

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.Published under an exclusive license by AIP 

 Publishing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000798221900004,

title = {Discharge rate characterization for submerged grains flowing through a 

 hopper using DEM-LBM simulations},

author = {Jianhua Fan and Li-Hua Luu and Pierre Philippe and Gildas Noury},

doi = {10.1016/j.powtec.2022.117421},

issn = {0032-5910},

year  = {2022},

date = {2022-05-01},

journal = {POWDER TECHNOLOGY},

volume = {404},

abstract = {Submerged granular flows through an orifice were investigated 

 numerically in the context of sinkhole occur-rences during a flood due 

 to the presence of underground conduits. To account for fluid-solid 

 interaction at the pore-scale, we use a numerical modelling that 

 combines the Discrete Element Method (DEM) for the solid par-ticles with 

 the Lattice Boltzmann Method (LBM) for the fluid dynamics. The numerical 

 setup studied is a sub-merged granular discharge from a hopper, which is 

 shown to be particularly sensitive to hydraulic boundary conditions. 

 With a given choice of configuration, we performed a parametric study by 

 varying particle diameters, fluid viscosity and hopper orifice size, 

 enabling the exploration of the Archimedes number over five orders of 

 magnitude. The solid discharge rates are shown to have self-similar 

 temporal evolutions and the grains at the or-ifice display self-similar 

 velocity profiles, normalized by the maximum velocity reached at the 

 center of the ori-fice. In this paper, we finally propose an extension 

 of the classical Beverloo law that takes into account the effect of 

 fluid entrainment by the downward granular flow.(c) 2022 Elsevier B.V. 

 All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000798925200010,

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 = {0035-8711},

year  = {2022},

date = {2022-05-01},

journal = {MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY},

volume = {513},

number = {4},

pages = {4929-4944},

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 alpha beta gamma-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{WOS:000793891300001,

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

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

doi = {10.1039/d2cp01056a},

issn = {1463-9076},

year  = {2022},

date = {2022-05-01},

journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},

volume = {24},

number = {20},

pages = {12346-12353},

abstract = {Recent experimental work revealed that the lifetime of the S-3 state of 

 protonated 7-azaindole is about ten times longer than that of protonated 

 6-azaindole. We simulated the nonradiative decay pathways of these 

 molecules using trajectory surface hopping dynamics after 

 photoexcitation into S-3 to elucidate the reason for this difference. 

 Both isomers mainly follow a common pi pi* relaxation pathway 

 involving multiple state crossings while coming down from S-3 to S-1 in 

 the subpicosecond time scale. However, the simulations reveal that the 

 excited-state topographies are such that while the 6-isomer can easily 

 access the region of nonadiabatic transitions, the internal conversion 

 of the 7-isomer is delayed by a pre-Dewar bond formation with a boat 

 conformation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000883226100001,

title = {Pulsated Herschel-Bulkley flows in two-dimensional channels: A model for 

 mucus clearance devices},

author = {Antoine Galko and Simon Gsell and Umberto D'Ortona and Laurent Morin and Julien Favier},

doi = {10.1103/PhysRevFluids.7.053301},

issn = {2469-990X},

year  = {2022},

date = {2022-05-01},

journal = {PHYSICAL REVIEW FLUIDS},

volume = {7},

number = {5},

abstract = {Pressure oscillations applied to human airways can help patients to 

 evacuate bronchial mucus, a highly non-Newtonian gel. To explore the 

 fluid mechanics aspects of these therapies, we perform numerical 

 simulations of pulsated non-Newtonian fluids in two-dimensional 

 channels. The fluid rheology is modeled with the Herschel-Bulkley law, 

 reproducing two essential nonlinear mechanical properties of the mucus, 

 namely, the yield-stress and shear-thinning/thickening properties. The 

 flow dynamics is simulated using the lattice-Boltzmann method over large 

 ranges of the three main nondimensional parameters, i.e., the pulsation 

 rate or Womersley number a, the flow index n quantifying the 

 shear-thinning/thickening effect, and the Bingham number controlling the 

 yield stress. The ratio between the fluctuating and average parts of the 

 oscillatory forcing is examined through three typical cases: a purely 

 oscillating flow, a weakly oscillating flow, and a strongly oscillating 

 flow. For each configuration, specific sets of parameters are found to 

 have a drastic effect on the dynamics of mucus plugs, which suggests new 

 therapeutic strategies for patients suffering from bronchial 

 obstructions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000832204400011,

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 = {1070-6631},

year  = {2022},

date = {2022-04-01},

journal = {PHYSICS OF FLUIDS},

volume = {34},

number = {4},

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{WOS:000746697400001,

title = {An experimental data-driven mass-spring model of flexible 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 = {1748-3182},

year  = {2022},

date = {2022-03-01},

journal = {BIOINSPIRATION & BIOMIMETICS},

volume = {17},

number = {2},

publisher = {IOP Publishing Ltd},

address = {TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND},

abstract = {Insect wings can undergo significant deformation during flapping motion 

 owing to inertial, elastic and aerodynamic forces. Changes in shape then 

 alter aerodynamic forces, resulting in a fully coupled fluid-structure 

 interaction (FSI) problem. Here, we present detailed three-dimensional 

 FSI simulations of deformable blowfly (Calliphora vomitoria) wings in 

 flapping flight. A wing model is proposed using a multi-parameter 

 mass-spring approach, chosen for its implementation simplicity and 

 computational efficiency. We train the model to reproduce static 

 elasticity measurements by optimizing its parameters using a genetic 

 algorithm with covariance matrix adaptation (CMA-ES). Wing models 

 trained with experimental data are then coupled to a high-performance 

 flow solver run on massively parallel supercomputers. Different features 

 of the modeling approach and the intra-species variability of elastic 

 properties are discussed. We found that individuals with different wing 

 stiffness exhibit similar aerodynamic properties characterized by 

 dimensionless forces and power at the same Reynolds number. We further 

 study the influence of wing flexibility by comparing between the 

 flexible wings and their rigid counterparts. Under equal prescribed 

 kinematic conditions for rigid and flexible wings, wing flexibility 

 improves lift-to-drag ratio as well as lift-to-power ratio and reduces 

 peak force observed during wing rotation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bufferand_2022,

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},

url = {https://doi.org/10.1088/1361-6587/ac4fac},

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

year  = {2022},

date = {2022-03-01},

journal = {Plasma Physics and Controlled Fusion},

volume = {64},

number = {5},

pages = {055001},

publisher = {IOP Publishing},

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{WOS:000751809800001c,

title = {Single-cell transcriptomics uncovers an instructive T-cell receptor role  in adult gamma delta T-cell lineage commitment},

author = {Sara Scaramuzzino and Delphine Potier and Robin Ordioni and Pierre Grenot and Dominique Payet-Bornet and Herve Luche and Bernard Malissen},

doi = {10.15252/embj.2021110023},

issn = {0261-4189},

year  = {2022},

date = {2022-02-17},

journal = {EMBO JOURNAL},

abstract = {After entering the adult thymus, bipotent T-cell progenitors give rise 

 to alpha beta or gamma delta T cells. To determine whether the gamma 

 delta T-cell receptor (TCR) has an instructive role in gamma delta 

 T-cell lineage commitment or only ``confirms'' a pre-established gamma 

 delta T-cell lineage state, we exploited mice lacking expression of LAT, 

 an adaptor required for gamma delta TCR signaling. Although these mice 

 showed a T-cell development block at the CD4(-)CD8(-) double-negative 

 third (DN3) stage, 0.3% of their DN3 cells expressed intermediate 

 levels of gamma delta TCR (further referred to as gamma delta(int)) at 

 their surface. Single-cell transcriptomics of LAT-deficient DN3 gamma 

 delta(int) cells demonstrated no sign of commitment to the gamma delta 

 T-cell lineage, apart from gamma delta TCR expression. Although the lack 

 of LAT is thought to tightly block DN3 cell development, we unexpectedly 

 found that 25% of LAT-deficient DN3 gamma delta(int) cells were 

 actively proliferating and progressed up to the DN4 stage. However, even 

 those cells failed to turn on the transcriptional program associated 

 with the gamma delta T-cell lineage. Therefore, the gamma delta TCR-LAT 

 signaling axis builds upon a yi5 T-cell uncommitted lineage state to 

 fully instruct adult gamma delta T-cell lineage specification.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2022,

title = {Mechanisms for recirculation cells in granular flows in rotating cylindrical rough tumblers},

author = {Umberto D'Ortona and Nathalie Thomas and Richard M. Lueptow},

url = {http://dx.doi.org/10.1103/PhysRevE.105.014901},

doi = {10.1103/physreve.105.014901},

issn = {2470-0053},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Physical Review E},

volume = {105},

number = {1},

publisher = {American Physical Society (APS)},

abstract = {Friction at the endwalls of partially-filled horizontal rotating tumblers induces curvature and axial drift of particle trajectories in the surface flowing layer. Here we describe the results of a detailed discrete element method study of the dry granular flow of monodisperse particles in threedimensional cylindrical tumblers with endwalls and cylindrical wall that can be either smooth or rough. Endwall roughness induces more curved particle trajectories, while a smooth cylindrical wall enhances drift near the endwall. This drift induces recirculation cells near the endwall. The use of mixed roughness (cylindrical wall and endwalls having different roughness) shows the influence of each wall on the drift and curvature of particle trajectories as well as the modification of the free surface topography. The effects act in opposite directions and have variable magnitude along the length of the tumbler such that their sum determines both direction of net drift and the recirculation cells. Near the endwalls, the dominant effect is always the endwall effect, and the axial drift for surface particles is toward the endwalls. For long enough tumblers, a counter-rotating cell occurs adjacent to each of the endwall cells having a surface drift toward the center because the cylindrical wall effect is dominant there. These cells are not dynamically coupled with the two endwall cells. The competition between the drifts induced by the endwalls and the cylindrical wall determines the width and drift amplitude for both types of cells. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{w14010062,

title = {Wind-Induced Resuspension and Transport of Contaminated Sediment from the Rove Canal into the Etang De Berre, France},

author = {Elena Alekseenko and Bernard Roux and Konstantin Kuznetsov},

url = {https://www.mdpi.com/2073-4441/14/1/62},

doi = {10.3390/w14010062},

issn = {2073-4441},

year  = {2022},

date = {2022-01-01},

journal = {Water},

volume = {14},

number = {1},

abstract = {The present study concerns the erosion and transport of severely contaminated sediments in a Canal. It begins in the context of an engineering project aimed to re-introduce a forced convection at the entrance of this Canal by pumping marine water. The local wind is often strong enough to overpass the resuspension threshold; thus, there is a serious risk of downstream contamination of a Mediterranean lagoon. So, the goal is to evaluate this risk as a function of the pumping rate; this contamination is transported by the fine suspended particles. Different scenarios are investigated to determine the downstream transport of suspensions in terms of runoff. These scenarios (of 24 h) contains a succession of 3 periods: constant wind speed, wind slowdown and calm, for two opposite wind directions. Special attention is devoted to the modeling of complex mechanisms of erosion and resuspension during wind periods, deposition during windless periods and sediment consolidation. The main results concern the total flux of the suspended particles through the exit of the Canal at the confluence with the lagoon. It is shown that even for moderate runoff (<6 m3/s) this total flux is large enough, not only during the wind period, but also after several hours of calm.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000697391500020,

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 = {0956-540X},

year  = {2022},

date = {2022-01-01},

journal = {GEOPHYSICAL JOURNAL INTERNATIONAL},

volume = {228},

number = {1},

pages = {337-354},

abstract = {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 percent 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{BHAIRAPURADA2022112049,

title = {A Lattice-Boltzmann study of premixed flames thermo-acoustic instabilities},

author = {Karthik Bhairapurada and Bruno Denet and Pierre Boivin},

url = {https://www.sciencedirect.com/science/article/pii/S0010218022000682},

doi = {https://doi.org/10.1016/j.combustflame.2022.112049},

issn = {0010-2180},

year  = {2022},

date = {2022-01-01},

journal = {Combustion and Flame},

volume = {240},

pages = {112049},

abstract = {We present possibly for the first time Lattice-Boltzmann numerical simulations of thermo-acoustic instabilities of premixed flames. We study flames interacting with an imposed acoustic field where flames submitted to a parametric instability can be observed, as well as plane flames re-stabilized by the acoustic forcing. Self-induced thermo-acoustic oscillations of flames propagating in narrow channels are also studied, indicating an unexpected dependency with the channel width. For both excited and self-excited flames, results confirm that Lattice-Boltzmann method can capture the complex coupling between flame dynamics and acoustics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000692550000006,

title = {Impact of Ni alloying on Fe-C martensite ageing: an atomistic  investigation},

author = {Paul Eymeoud and Liangzhao Huang and Philippe Maugis},

doi = {10.1016/j.scriptamat.2021.114182},

issn = {1359-6462},

year  = {2021},

date = {2021-12-01},

journal = {Scripta materialia},

volume = {205},

abstract = {We propose a computational investigation of Ni-alloying impact on Fe-C 

 martensite ageing, at the atomic scale. Using the Climbing Image Nudged 

 Elastic Band technique, we showed the repulsive nature of NiC pairwise 

 interactions in alpha-iron, and demonstrated that Ni alloying lowers the 

 migration energies and force dipole tensor components associated to an 

 interstitial carbon in alpha-iron. Computed values of pair wise 

 interactions, migration energies and dipole components were used to 

 implement a Kinetic Monte Carlo approach. We found that Ni alloying: (i) 

 has negligible impact on martensite thermodynamical stability, (ii) 

 accelerates ageing kinetics, by increasing carbon diffusivity. (C) 2021 

 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{coratger:hal-03424286,

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

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

url = {https://hal.archives-ouvertes.fr/hal-03424286},

doi = {10.1063/5.0064944},

year  = {2021},

date = {2021-11-01},

urldate = {2021-11-01},

journal = {Physics of Fluids},

volume = {33},

number = {11},

pages = {115112},

publisher = {American Institute of Physics},

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{wang:hal-03438869,

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},

url = {https://hal.archives-ouvertes.fr/hal-03438869},

doi = {10.1063/5.0073178},

year  = {2021},

date = {2021-11-01},

urldate = {2021-11-01},

journal = {Physics of Fluids},

volume = {33},

number = {11},

pages = {116107},

publisher = {American Institute of Physics},

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{2021j,

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 De A Backer and C S Becquart and S Markelj and C Grisolia},

url = {https://doi.org/10.1088/1741-4326/ac2abc},

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

year  = {2021},

date = {2021-10-01},

volume = {61},

number = {12},

pages = {126003},

publisher = {IOP Publishing},

abstract = {In this work, the deuterium (D) retention in plasma facing components of the divertor of ITER is estimated. Three scenarios are simulated with 3 different surface temperatures, 1456 K, 870 K and 435 K. They represent the exposure of different parts of the divertor during an attached plasma. Our 1D rate equation code MHIMS (migration of hydrogen in materials) is used to model the retention in the super-saturated layer formed in the first 10 nm: the D retention integrated in this 10 nm-layer is ≈1019 D m−2 for the coldest scenarios. It is also used to differentiate the evolution of deuterium retention during pulsed and continuous plasma exposures which shows that: (i) there is a retention during the ramp-down in the first 10 μm which is released during the ramp up and (ii) the bulk retention is not affected by the cycling of plasma exposure. The concentration of mobile deuterium in the implantation zone is used as an input of our finite element code FESTIM (finite element simulation of tritium in materials) which is used to assess the deuterium retention and migration in the 2D complex geometry of the actively cooled plasma facing components. In the end, this work enable to determine the three following macroscopic quantities: the total deuterium retention, the permeation flux to the cooling pipe and the desorption flux from the toroidal edges of the components. It is shown that (i) the coldest scenario leads to the highest retention despite the lowest exposure flux which has already been observed in past retention studies, (ii) the permeation to the cooling pipes happens after few thousands of seconds only for the hottest scenario, (iii) the release of deuterium from the toroidal edges is a small fuel recycling source.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Truong_2021,

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

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

url = {https://doi.org/10.1088/1748-3190/ac2f56},

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

year  = {2021},

date = {2021-10-01},

urldate = {2021-10-01},

journal = {Bioinspiration & Biomimetics},

publisher = {IOP Publishing},

abstract = {Insect wings can undergo significant deformation during flapping motion owing to inertial, elastic and aerodynamic forces. Changes in shape then alter aerodynamic forces, resulting in a fully coupled fluid–structure interaction (FSI) problem. Here, we present detailed three-dimensional FSI simulations of deformable blowfly (Calliphora vomitoria) wings in flapping flight. A wing model is proposed using a multi-parameter mass-spring approach, chosen for its implementation simplicity and computational efficiency. We train the model to reproduce static elasticity measurements by optimizing its parameters using a genetic algorithm with covariance matrix adaptation (CMA-ES). Wing models trained with experimental data are then coupled to a high-performance flow solver run on massively parallel supercomputers. Different features of the modeling approach and the intra-species variability of elastic properties are discussed. We found that individuals with different wing stiffness exhibit similar aerodynamic properties characterized by dimensionless forces and power at the same Reynolds number. We further study the influence of wing flexibility by comparing between the flexible wings and their rigid counterparts. Under equal prescribed kinematic conditions for rigid and flexible wings, wing flexibility improves lift-to-drag ratio as well as lift-to-power ratio and reduces peak force observed during wing rotation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gomes_2021,

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},

url = {http://dx.doi.org/10.1063/5.0040939},

doi = {10.1063/5.0040939},

issn = {1089-7682},

year  = {2021},

date = {2021-08-01},

journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science},

volume = {31},

number = {8},

pages = {083104},

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{Das_2021,

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},

url = {http://dx.doi.org/10.1063/5.0057168},

doi = {10.1063/5.0057168},

issn = {1089-7666},

year  = {2021},

date = {2021-08-01},

journal = {Physics of Fluids},

volume = {33},

number = {8},

pages = {081905},

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, 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 sensitive dependence of intermediate shapes on type of pulse and the 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, that seems to be a characteristics 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. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000692557000001,

title = {Lattice-Boltzmann-based large-eddy simulation of high-rise building  aerodynamics with inlet turbulence reconstruction},

author = {Elisa Buffa and Jerome Jacob and Pierre Sagaut},

doi = {10.1016/j.jweia.2021.104560},

issn = {0167-6105},

year  = {2021},

date = {2021-05-01},

journal = {Journal of wind engineering and industrial aerodynamics},

volume = {212},

abstract = {A Lattice-Boltzmann-based Large-Eddy Simulation approach for wind load 

 prediction on high-rise building is proposed and validated. An extension 

 of the original incompressible Synthetic Eddy Method to reconstruct 

 inlet turbulence is proposed within the Lattice-Boltzmann framework, 

 including a low-noise frozen density variant. Extensive successful 

 comparisons with experimental data are carried out, for both quantities 

 defined on the building surface and in its wake. A detailed sensitivity 

 analysis of the results with respect to inlet turbulence reconstruction, 

 boundary conditions at the building surface and grid resolution is also 

 provided. An almost unique set of comparisons with experimental data is 

 presented, including mean and rms values, spectra, but also peak values 

 of pressure at the building surface.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Xiang_2021,

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},

url = {http://dx.doi.org/10.3847/1538-4357/abdab5},

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

issn = {1538-4357},

year  = {2021},

date = {2021-03-01},

journal = {The Astrophysical Journal},

volume = {909},

number = {2},

pages = {125},

publisher = {American Astronomical Society},

abstract = {Over half of disk galaxies are barred, yet the mechanisms for bar formation and the life-time 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 (IFU) 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{PhysRevFluids.6.024601,

title = {Laboratory model for plastic fragmentation in the turbulent ocean},

author = {Christophe Brouzet and Raphaël Guiné and Marie-Julie Dalbe and Benjamin Favier and Nicolas Vandenberghe and Emmanuel Villermaux and Gautier Verhille},

url = {https://link.aps.org/doi/10.1103/PhysRevFluids.6.024601},

doi = {10.1103/PhysRevFluids.6.024601},

year  = {2021},

date = {2021-02-01},

journal = {Phys. Rev. Fluids},

volume = {6},

pages = {024601},

publisher = {American Physical Society},

abstract = {The fragmentation of solid objects in turbulence is of paramount importance in a large number of situations, especially for marine plastic pollution where small plastic debris are formed by the fragmentation of plastic litter under hydrodynamic forces. Up to now, investigations have focused on the fragmentation of particle aggregates in turbulent flows. Here we study the fragmentation of a single deformable object that behaves elastically up to breakage, in the inertial range of turbulence. Using laboratory experiments with glass fibers as a model system, complemented by numerical simulations and theoretical analyses, we exhibit a comprehensive fragmentation scenario, further modeled by an evolution equation. Our results demonstrate that the fragmentation process is limited at small scales by a physical cutoff length originating from the fluid-structure interactions between the objects and the turbulence, and therefore independent of the brittleness of the fibers. This scenario leads to the accumulation of fragments with a typical length slightly longer than the cutoff scale, as smaller fragments are too short to be deformed and broken by the turbulence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/ejoc.202001599,

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},

url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/ejoc.202001599},

doi = {https://doi.org/10.1002/ejoc.202001599},

year  = {2021},

date = {2021-01-01},

journal = {European Journal of Organic Chemistry},

volume = {2021},

number = {4},

pages = {512-512},

abstract = {The Front Cover shows a chiral double decker porphyrin cage, which has been resolved into enantiomers (red and blue structures). The compound was characterized by various physical techniques, including X-ray and circular dichroism (spectra in the center). The porphyrin cage compound forms well-defined self-assembled monolayers on HOPG surfaces, which are visible by scanning tunneling microscopy (background). The binding of a guest (viologen) in one of the cages of the compound leads to a contraction of the other cage (indicated by the white wiggles), resulting in a greatly reduced guest binding in the latter cage (negative allosteric effect). More information can be found in the Full Paper by Roeland J.M. Nolte et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{CAI2021109995,

title = {Coupling of turbulence wall models and immersed boundaries on Cartesian grids},

author = {Shang-Gui Cai and Johan Degrigny and Jean-François Boussuge and Pierre Sagaut},

url = {https://www.sciencedirect.com/science/article/pii/S0021999120307695},

doi = {https://doi.org/10.1016/j.jcp.2020.109995},

issn = {0021-9991},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Computational Physics},

volume = {429},

pages = {109995},

abstract = {An improved coupling of immersed boundary method and turbulence wall models on Cartesian grids is proposed, for producing smooth wall surface pressure and skin friction at high Reynolds numbers. Spurious oscillations are frequently observed on these quantities with most immersed boundary wall modeling methods, especially for the skin friction which is found to be very sensitive to the solid surface's position and orientation against the Cartesian grids. The problem originates from the irregularity of the wall distance on the stair-step grid boundaries where the immersed boundary conditions are applied. To reduce this directional error, several modifications are presented to enhance the near wall solution. First, the commonly used interpolation for the flow velocity is replaced by one for the friction velocity, which has much less variation near wall. The concept of using a fictitious point to retrieve flow fields in the wall normal direction is abandoned and the interpolation is performed in the wall parallel plane with existing fluid points. Secondly, the velocity gradients at the approximated boundary are computed with advanced schemes and the normal gradient of the tangential velocity is reconstructed from the wall laws. To further protect the near wall solution, the normal velocity gradient and the working viscosity from the Spalart-Allmaras turbulence model are enforced by their theoretical solutions in the interior fluid close to the wall. Additionally, various post-processing algorithms for reconstructing wall surface quantities and force integrations are investigated. Other related factors are also discussed for their effects on the results. The validity of present method has been demonstrated through numerical benchmark tests on a flat plate at zero pressure gradient, both aligned and inclined with respect to the grid, as well as aerodynamic cases of NACA 23012 airfoil and NASA trap wing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MAUGIS2021113632,

title = {Stability of Zener order in martensite: an atomistic evidence},

author = {Philippe Maugis and Damien Connétable and Paul Eyméoud},

url = {https://www.sciencedirect.com/science/article/pii/S1359646220307442},

doi = {https://doi.org/10.1016/j.scriptamat.2020.113632},

issn = {1359-6462},

year  = {2021},

date = {2021-01-01},

journal = {Scripta Materialia},

volume = {194},

pages = {113632},

abstract = {Martensite is a supersaturated solid solution of carbon in body-centered iron wherein interstitial carbon atoms preferentially occupy a single octahedral sublattice. Despite a century of research, the mechanism of this long-range ordering is still a subject of debate. Recently, Zener’s theory of ordering was challenged both experimentally and theoretically. In an attempt to settle the controversy, we investigated by density functional theory the ground states of Fe-C configurations having various degrees of order. We conclude that the fully Zener-ordered configurations are always the most stable energetically, thus confirming Zener’s theory. Comparison with mean-field elasticity and Ising-type modelling supports the elastic origin of Zener ordering.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tayyab:hal-03160901,

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

author = {M Tayyab and S Zhao and Pierre Boivin},

url = {https://hal.archives-ouvertes.fr/hal-03160901},

doi = {10.1063/5.0038089},

year  = {2021},

date = {2021-01-01},

journal = {Physics of Fluids},

volume = {33},

number = {3},

pages = {031701},

publisher = {American Institute of Physics},

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 modelling of reactive flows is competitive, with around 1000cpuh required to simulate one residence time in the 1,5m burner. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MANDAL2021110810,

title = {Sticky islands in stochastic webs and anomalous chaotic cross-field particle transport by E×B electron drift instability},

author = {D Mandal and Y Elskens and X Leoncini and N Lemoine and F Doveil},

url = {https://www.sciencedirect.com/science/article/pii/S0960077921001624},

doi = {https://doi.org/10.1016/j.chaos.2021.110810},

issn = {0960-0779},

year  = {2021},

date = {2021-01-01},

journal = {Chaos, Solitons & Fractals},

volume = {145},

pages = {110810},

abstract = {The E×B electron drift instability, present in many plasma devices, is an important agent in cross-field particle transport. In presence of a resulting low frequency electrostatic wave, the motion of a charged particle becomes chaotic and generates a stochastic web in phase space. We define a scaling exponent to characterise transport in phase space and we show that the transport is anomalous, of super-diffusive type. Given the values of the model parameters, the trajectories stick to different kinds of islands in phase space, and their different sticking time power-law statistics generate successive regimes of the super-diffusive transport.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{FRANGIEH2021103383,

title = {Fuelbreak effectiveness against wind-driven and plume-dominated fires: A 3D numerical study},

author = {Nicolas Frangieh and Gilbert Accary and Jean-Louis Rossi and Dominique Morvan and Sofiane Meradji and Thierry Marcelli and François-Joseph Chatelon},

url = {https://www.sciencedirect.com/science/article/pii/S0379711221001247},

doi = {https://doi.org/10.1016/j.firesaf.2021.103383},

issn = {0379-7112},

year  = {2021},

date = {2021-01-01},

journal = {Fire Safety Journal},

volume = {124},

pages = {103383},

abstract = {The effectiveness of a fuelbreak, created in a homogeneous grassland on a flat terrain, was studied numerically. The analysis relies on 3D numerical simulations that were performed using a detailed physical-fire-model (FIRESTAR3D) based on a multiphase formulation. To avoid border effects, calculations were carried out by imposing periodic boundary conditions along the two lateral sides of the computational domain, reproducing that way a quasi-infinitely long fire front. A total of 72 simulations were carried out for various wind speeds, fuel heights, and fuelbreak widths, which allowed to cover a large spectrum of fire behaviour, ranging from plume-dominated fires to wind-driven fires. The results were classified in three main categories: 1- “Propagation” if fire crossed the fuelbreak with a continuous fire front, 2- “Overshooting” and “Marginal” if fire marginally crosses the fuelbreak with the formation of burning pockets, and 3- “No propagation” if fire does not cross at all the fuelbreak. The ratio of fuelbreak width to fuel height, marking the “Propagation”/“No propagation” transition, was found to be scaled with Byram's convection number Nc as 75.07 × Nc−0.46. The numerical results were also compared to an operational wildfire engineering tool (DIMZAL) dedicated to fuelbreaks dimensioning.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boivin:hal-03276189,

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

author = {Pierre Boivin and M Tayyab and S Zhao},

url = {https://hal.archives-ouvertes.fr/hal-03276189},

doi = {10.1063/5.0057352},

year  = {2021},

date = {2021-01-01},

journal = {Physics of Fluids},

volume = {33},

number = {7},

pages = {071703},

publisher = {American Institute of Physics},

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{EYMEOUD2021110547,

title = {How to take into account local concentration in Ising-based Monte-Carlo: illustration with zirconium hydrides},

author = {Paul Eyméoud and Fabienne Ribeiro and Rémy Besson and Guy Tréglia},

url = {https://www.sciencedirect.com/science/article/pii/S0927025621002743},

doi = {https://doi.org/10.1016/j.commatsci.2021.110547},

issn = {0927-0256},

year  = {2021},

date = {2021-01-01},

journal = {Computational Materials Science},

volume = {197},

pages = {110547},

abstract = {We present a detailed methodology for treating local concentration dependency of pairwise interactions in Ising-based Monte-Carlo. The procedure is described through the example of interstitial ordering processes in zirconium hydrides, studied by canonical Monte-Carlo based on a concentration-dependent Tight-Binding Ising Model. The path leads to build a phase diagram of hydrogen-vacancy ordering on interstitial tetrahedral sublattice of face-centered cubic Zr-H.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{petac:hal-03262627,

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},

url = {https://hal.archives-ouvertes.fr/hal-03262627},

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

year  = {2021},

date = {2021-01-01},

journal = {JCAP},

volume = {08},

pages = {031},

abstract = {Signal predictions for galactic dark matter (DM) searches often rely on assumptions regarding the DM phase-space distribution function (DF) in halos. This applies to both particle (e.g. p-wave suppressed or Sommerfeld-enhanced annihilation, scattering off atoms, etc.) and macroscopic DM candidates (e.g. microlensing of primordial black holes). As experiments and observations improve in precision, better assessing theoretical uncertainties becomes pressing in the prospect of deriving reliable constraints on DM candidates or trustworthy hints for detection. Most reliable predictions of DFs in halos are based on solving the steady-state collisionless Boltzmann equation (e.g. Eddington-like inversions, action-angle methods, etc.) consistently with observational constraints. One can do so starting from maximal symmetries and a minimal set of degrees of freedom, and then increasing complexity. Key issues are then whether adding complexity, which is computationally costy, improves predictions, and if so where to stop. Clues can be obtained by making predictions for zoomed-in hydrodynamical cosmological simulations in which one can access the true (coarse-grained) phase-space information. Here, we test an axisymmetric extension of the Eddington inversion to predict the full DM DF from its density profile and the total gravitational potential of the system. This permits to go beyond spherical symmetry, and is a priori well suited for spiral galaxies. We show that axisymmetry does not necessarily improve over spherical symmetry because the (observationally unconstrained) angular momentum of the DM halo is not generically aligned with the baryonic one. Theoretical errors are similar to those of the Eddington inversion though, at the 10–20% level for velocity-dependent predictions related to particle DM searches in spiral galaxies. We extensively describe the approach and comment on the results.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/gji/ggab343,

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},

url = {https://doi.org/10.1093/gji/ggab343},

doi = {10.1093/gji/ggab343},

issn = {0956-540X},

year  = {2021},

date = {2021-01-01},

journal = {Geophysical Journal International},

volume = {228},

number = {1},

pages = {337-354},

abstract = {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{articlem,

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

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

doi = {10.1063/5.0048563},

year  = {2021},

date = {2021-01-01},

journal = {Physics of Fluids},

volume = {33},

pages = {041703},

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{article,

title = {First-Principle Investigations on the Electronic and Transport Properties of PbBi2Te2X2 (X = S/Se/Te) Monolayers},

author = {Weiliang Ma and Jing Tian and Pascal Boulet and Marie-Christine Record},

doi = {10.3390/nano11112979},

year  = {2021},

date = {2021-01-01},

journal = {Nanomaterials},

volume = {11},

pages = {2979},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{yang:hal-03126595,

title = {Highly accurate monotonicity-preserving Semi-Lagrangian scheme for Vlasov-Poisson Simulations},

author = {C Yang and Michel Mehrenberger},

url = {https://hal.archives-ouvertes.fr/hal-03126595},

doi = {10.1016/j.jcp.2021.110632},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Journal of Computational Physics},

publisher = {Elsevier},

abstract = {In this paper, we study a high accurate monotonicity-preserving (MP) Semi-Lagrangian scheme for Vlasov-Poisson simulations. The classical Semi-Lagrangian scheme is known to be high accurate and free from CFL condition, but it does not satisfy local maximum principle. To remedy this drawback, using the conservative form of the Semi-Lagrangian scheme, we recast existing MP schemes for the numerical flux in a common framework, and then substitute the local minimum/maximum by some "better" guess, in order to avoid as much as possible loss of accuracy and clipping near extrema, while keeping the monotonicity on monotone portions. With the limiter, on the one hand, the scheme keeps the good properties of the unlimited scheme: it is conservative, free from CFL condition and high accurate. On the other hand, for locally monotonic data, the monotonicity of the solution is preserved. Numerical tests are made on free transport equation and Vlasov-Poisson system to illustrate the robustness of our method. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{CRPHYS_2021__22_S2_111_0,

title = {Sub-picosecond C=C bond photo-isomerization: evidence for the role of excited state mixing},

author = {Damianos Agathangelou and Partha Pratim Roy and Maria del Carmen Marin and Nicolas Ferré and Massimo Olivucci and Tiago Buckup and J'er'emie L'eonard and Stefan Haacke}},

editor = {Académie des sciences, Paris},

url = {https://comptes-rendus.academie-sciences.fr/physique/articles/10.5802/crphys.41/},

doi = {10.5802/crphys.41},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Comptes Rendus. Physique},

volume = {22},

pages = {111--138},

abstract = {Sub-picosecond photo-isomerization is the major primary process of energy conversion in retinal proteins and has as such been in the focus of extensive theoretical and experimental work over the past decades. In this review article, we revisit the long-standing question as to how the protein tunes the isomerization speed and quantum yield. We focus on our recent contributions to this field, which underscore the concept of a delicate mixing of reactive and non-reactive excited states, as a result of steric properties and electrostatic interactions with the protein environment. Further avenues and new approaches are outlined which hold promise for advancing our understanding of these intimately coupled chromophore-protein systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{abiola:hal-03426788,

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

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

editor = {The Royal Society of Chemistry},

url = {http://dx.doi.org/10.1039/D1SC05077J},

doi = {10.1039/D1SC05077J},

year  = {2021},

date = {2021-01-01},

journal = {Chem. Sci.},

volume = {12},

pages = {15239-15252},

publisher = {Chemical Science },

abstract = {Light-to-heat conversion materials generate great interest due to their widespread applications{,} notable exemplars being solar energy harvesting and photoprotection. Another more recently identified potential application for such materials is in molecular heaters for agriculture{,} whose function is to protect crops from extreme cold weather and extend both the growing season and the geographic areas capable of supporting growth{,} all of which could help reduce food security challenges. To address this demand{,} a new series of phenolic-based barbituric absorbers of ultraviolet (UV) radiation has been designed and synthesised in a sustainable manner. The photophysics of these molecules has been studied in solution using femtosecond transient electronic and vibrational absorption spectroscopies{,} allied with computational simulations and their potential toxicity assessed by in silico studies. Following photoexcitation to the lowest singlet excited state{,} these barbituric absorbers repopulate the electronic ground state with high fidelity on an ultrafast time scale (within a few picoseconds). The energy relaxation pathway includes a twisted intramolecular charge-transfer state as the system evolves out of the Franck–Condon region{,} internal conversion to the ground electronic state{,} and subsequent vibrational cooling. These barbituric absorbers display promising light-to-heat conversion capabilities{,} are predicted to be non-toxic{,} and demand further study within neighbouring application-based fields.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MAGNICO202133915,

title = {Molecular dynamics study on water and hydroxide transfer mechanisms in PSU-g-alkyl-TMA membranes at low hydration: Effect of side chain length},

author = {Pierre Magnico},

url = {https://www.sciencedirect.com/science/article/pii/S0360319921027221},

doi = {https://doi.org/10.1016/j.ijhydene.2021.07.081},

issn = {0360-3199},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {International Journal of Hydrogen Energy},

volume = {46},

number = {68},

pages = {33915-33933},

abstract = {Molecular dynamics simulations with anion exchange membranes (alkyl trimethyl ammonium grafted onto polysulfone) are performed to investigate the influence of the spacer length on the transport properties, on the molecular exchange mechanisms between the functional group and the aqueous phase and on the hydrogen bond network. This is especially insightful that in this work the hydration number is small. In this condition the aqueous phase must be thought as an assembly of small clusters. The results show an unexpected dependence of the water and hydroxide (OH) diffusivity on the temperature and the water uptake. The distribution of the cluster size bonded to OH explain partially the OH diffusivity. “Hopping” and “caging” motions are observed with the self-part of the Van Hove functions even at high temperature. The characteristic time of the survival probability correlation function around the functional groups is a decreasing function of the alkyl length. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{refId0d,

title = {On the reflection of time-domain acoustic spherical waves by a sinusoidal diffraction grating},

author = {Guochao} {Gao and Paul} {Cristini and Nathalie} {Favretto-Cristini and Carole} {Deumié},

url = {https://doi.org/10.1051/aacus/2020033},

doi = {10.1051/aacus/2020033},

year  = {2021},

date = {2021-01-01},

journal = {Acta Acust.},

volume = {5},

pages = {6},

abstract = {This work reports on some results obtained from numerical simulations of time-domain acoustic wave propagation in the presence of a periodically rough interface. Emphasis is put on the structure of the reflected signals in the presence of a sinusoidal grating. More specifically, we investigate the effect of the frequency bandwidth of the emitted signal and the effect of the incident wavefront sphericity on the signals reflected from the rough interface and associated with the different diffraction orders.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articled,

title = {Parallel modeling of wildfires using efficient solvers for ill-conditioned linear systems},

author = {Oleg Bessonov and Sofiane Meradji},

doi = {10.1007/s11227-021-03632-8},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Supercomputing},

abstract = {Numerical simulation of multi-physical processes requires a lot of processor time, 

especially when solving ill-conditional linear systems arising in fluid dynamics 

problems. This paper is devoted to the development of efficient parallel methods for 

such systems for FireStar3D wildfire modeling code. Two alternative approaches 

are discussed and analyzed, based on the MILU-preconditioned conjugate gradient 

method and on the algebraic multigrid, respectively. The main difficulties of paral-

lelizing these methods are considered and solutions are presented: in the first case, 

nested twisted factorization with a staircase pipelining, and in the second, a multi-

color technique for a new smoother for strongly anisotropic grids. A novel quasi-

geometric interpolation technique is presented for solving the problem of positive 

off-diagonal matrix entries in the multigrid. The limits of applicability of the meth-

ods are determined depending on their flexibility, robustness and parallelization 

capabilities. The performance comparison demonstrates the superiority of the new 

methods over the widely used variants of the traditional conjugate gradient method.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gallo_2020,

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 WEST the team},

url = {https://doi.org/10.1088%2F1741-4326%2Fabb95b},

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

year  = {2020},

date = {2020-11-01},

journal = {Nuclear Fusion},

volume = {60},

number = {12},

pages = {126048},

publisher = {IOP Publishing},

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{Lacroix_2020,

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

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

url = {https://doi.org/10.1088%2F1475-7516%2F2020%2F10%2F031},

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

year  = {2020},

date = {2020-10-01},

journal = {Journal of Cosmology and Astroparticle Physics},

volume = {2020},

number = {10},

pages = {031--031},

publisher = {IOP Publishing},

abstract = {Reducing theoretical uncertainties in Galactic dark matter (DM) searches is an important challenge as several experiments are now delving into the parameter space relevant to popular (particle or not) candidates. Since many DM signal predictions rely on the knowledge of the DM velocity distribution—direct searches, capture by stars, p-wave-suppressed or Sommerfeld-enhanced annihilation rate, microlensing of primordial black holes, etc—it is necessary to assess the accuracy of our current theoretical handle. Beyond Maxwellian approximations or ad-hoc extrapolations of fits on cosmological simulations, approaches have been proposed to self-consistently derive the DM phase-space distribution only from the detailed mass content of the Galaxy and some symmetry assumptions (e.g. the Eddington inversion and its anisotropic extensions). Although theoretically sound, these methods are still based on simplifying assumptions and their relevance to real galaxies can be questioned. In this paper, we use zoomed-in cosmological simulations to quantify the associated uncertainties. Assuming isotropy, we predict the speed distribution and its moments from the DM and baryonic content measured in simulations, and compare them with the true ones. Taking as input galactic mass models fitted on full simulation data, we reach a predictivity down to ∼ 10% for some velocity-related observables, significantly better than some Maxwellian models. This moderate theoretical error is particularly encouraging at a time when stellar surveys like the Gaia mission should allow us to improve constraints on Galactic mass models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang_2020,

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},

url = {http://dx.doi.org/10.3847/1538-4357/ab7fad},

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

issn = {1538-4357},

year  = {2020},

date = {2020-04-01},

journal = {The Astrophysical Journal},

volume = {893},

number = {1},

pages = {19},

publisher = {American Astronomical Society},

abstract = {Bars in disc-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 disc-dominated galaxies with centrally suppressed SFR frequently host a bar. Here we investigate possible causes for the suppression of central SFR in such cases. We compare physical properties of a sample of disc-dominated barred galaxies with high central SFR (HC galaxies) with those of a sample of disc-dominated barred galaxies with low central SFR (LC galaxies). We find that the two samples have on average similar HI content and bars of similar strength. But we also find that the HCs have bluer colors than 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{PhysRevFluids.5.043602,

title = {Shape transition and hydrodynamics of vesicles in tube flow},

author = {Paul G Chen and J M Lyu and M Jaeger and M Leonetti},

url = {https://link.aps.org/doi/10.1103/PhysRevFluids.5.043602},

doi = {10.1103/PhysRevFluids.5.043602},

year  = {2020},

date = {2020-04-01},

journal = {Phys. Rev. Fluids},

volume = {5},

pages = {043602},

publisher = {American Physical Society},

abstract = {The steady motion and deformation of a lipid-bilayer vesicle translating through a circular tube in low Reynolds number pressure-driven flow are investigated numerically using an axisymmetric boundary element method. This fluid-structure interaction problem is determined by three dimensionless parameters: reduced volume (a measure of the vesicle asphericity), geometric confinement (the ratio of the vesicle effective radius to the tube radius), and capillary number (the ratio of viscous to bending forces). The physical constraints of a vesicle—fixed surface area and enclosed volume when it is confined in a tube—determine critical confinement beyond which it cannot pass through without rupturing its membrane. The simulated results are presented in a wide range of reduced volumes [0.6, 0.98] for different degrees of confinement; the reduced volume of 0.6 mimics red blood cells. We draw a phase diagram of vesicle shapes and propose a shape transition line separating the parachutelike shape region from the bulletlike one in the reduced volume versus confinement phase space. We show that the shape transition marks a change in the behavior of vesicle mobility, especially for highly deflated vesicles. Most importantly, high-resolution simulations make it possible for us to examine the hydrodynamic interaction between the wall boundary and the vesicle surface at conditions of very high confinement, thus providing the limiting behavior of several quantities of interest, such as the thickness of lubrication film, vesicle mobility and its length, and the extra pressure drop due to the presence of the vesicle. This extra pressure drop holds implications for the rheology of dilute vesicle suspensions. Furthermore, we present various correlations and discuss a number of practical applications. The results of this work may serve as a benchmark for future studies and help devise tube-flow experiments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lemasquerier2020,

title = {Remote determination of the shape of Jupiter’s vortices from laboratory experiments},

author = {Daphné Lemasquerier; Giulio Facchini; Benjamin Favier ; Michael Le Bars},

url = {https://doi.org/10.1038/s41567-020-0833-9},

doi = {10.1038/s41567-020-0833-9},

year  = {2020},

date = {2020-03-16},

journal = {Nature Physics},

abstract = {Jupiter’s dynamics shapes its cloud patterns but remains largely unknown below this natural observational barrier. Unravelling the underlying three-dimensional flows is thus a primary goal for NASA’s ongoing Juno mission, which was launched in 2011. Here, we address the dynamics of large Jovian vortices using laboratory experiments complemented by theoretical and numerical analyses. We determine the generic force balance responsible for their three-dimensional pancake-like shape. From this, we define scaling laws for their horizontal and vertical aspect ratios as a function of the ambient rotation, stratification and zonal wind velocity. For the Great Red Spot in particular, our predicted horizontal dimensions agree well with measurements at the cloud level since the Voyager mission in 1979. We also predict the Great Red Spot’s thickness, which is inaccessible to direct observation. It has remained surprisingly constant despite the observed horizontal shrinking. Our results now await comparison with upcoming Juno observations.

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PhysRevFluids.5.024801,

title = {Coupled convection and internal gravity waves excited in water around its density maximum at 4°C},

author = {P Léard and B Favier and P Le Gal and M Le Bars},

url = {https://link.aps.org/doi/10.1103/PhysRevFluids.5.024801},

doi = {10.1103/PhysRevFluids.5.024801},

year  = {2020},

date = {2020-02-01},

journal = {Phys. Rev. Fluids},

volume = {5},

pages = {024801},

publisher = {American Physical Society},

abstract = {Coupled mixed convective and stratified systems are common in natural flows. To study experimentally the associated dynamics, we use a singular property of water: its nonlinear equation of state is characterized by a maximum density close to 4°C. By heating the top of a tank at 35°C and cooling the bottom at 0°C, a two-layer configuration spontaneously appears. The convective motion in the bottom layer consists mostly of a large-scale circulation and rising cold plumes. This turbulent flow generates propagating internal gravity waves in the upper stably stratified layer. Particle image velocimetry measurements are performed and spectral characteristics of the convection and internal gravity waves are presented. An horizontal large-scale reversing flow in the stratified layer is observed which is viscously driven by a third, intermediate layer. This buffer layer is located between the convective and stratified layers and is thermally coupled with the convective one, hence sustaining a strong horizontal shear. Three-dimensional direct numerical simulations with geometry and physical parameters close to the experimental ones corroborate our experimental results.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nespoli_2020,

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

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

url = {https://doi.org/10.1088/1741-4326/ab6f1e},

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

year  = {2020},

date = {2020-02-01},

journal = {Nuclear Fusion},

volume = {60},

number = {4},

pages = {046002},

publisher = {IOP Publishing},

abstract = {Plasma filaments generated by turbulence in the scrape-off layer are sometimes observed in experiments and simulations to disconnect from the target plate in the vicinity of the X-point, resulting in a ‘quiescent zone’ with reduced fluctuations, possibly affecting the fluctuating part of the divertor heat loads. This phenomena is usually explained by the flux tubes squeezing, induced by flux expansion, down to scales where collisions dominate. In this work, we consider an additional mechanism spontaneously arising at the X-point: the poloidal shear in radial velocity. Through a simple model, tested against 3D global turbulence simulations, we quantify the effectiveness of this disconnection mechanism and identify ways to control it.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ISI:000500816900007,

title = {LONG-TIME BEHAVIOR OF SECOND ORDER LINEARIZED VLASOV-POISSON EQUATIONS 

 NEAR A HOMOGENEOUS EQUILIBRIUM},

author = {Joackim Bernier and Michel Mehrenberger},

doi = {10.3934/krm.2020005},

issn = {1937-5093},

year  = {2020},

date = {2020-02-01},

journal = {KINETIC AND RELATED MODELS},

volume = {13},

number = {1},

pages = {129-168},

publisher = {AMER INST MATHEMATICAL SCIENCES-AIMS},

address = {PO BOX 2604, SPRINGFIELD, MO 65801-2604 USA},

abstract = {The asymptotic behavior of the solutions of the second order linearized 

 Vlasov-Poisson system around homogeneous equilibria is derived. It 

 provides a fine description of some nonlinear and multidimensional 

 phenomena such as the existence of Best frequencies. Numerical results 

 for the 1D x 1D and 2D x 2D Vlasov-Poisson system illustrate the 

 effectiveness of this approach.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ISI:000500812100001,

title = {Natural poloidal asymmetry and neoclassical transport of impurities in 

 tokamak plasmas},

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

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

issn = {0741-3335},

year  = {2020},

date = {2020-02-01},

journal = {PLASMA PHYSICS AND CONTROLLED FUSION},

volume = {62},

number = {2},

publisher = {IOP PUBLISHING LTD},

address = {TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND},

abstract = {The neoclassical transport of impurities is investigated for a plasma 

 without toroidal rotation nor anisotropic ion temperature. It is shown 

 that a natural poloidal asymmetry of the impurity density exists in this 

 case, and that it can be described with a simple analytical model. The 

 poloidal asymmetry tends naturally to cancel as the impurity profile 

 evolves towards its steady state, so that the main effect of the 

 poloidal asymmetry is to slow down the impurity flux compared to its 

 predicted value without poloidal asymmetry. The contribution of the 

 asymmetries of the electrostatic potential and of the main ion density 

 can be included in the analytical derivation, thus forming a 

 self-consistent description of the neoclassical impurity flux together 

 with its poloidal distribution. Numerical simulations with a non linear 

 fluid code confirm the analytical findings, showing that the 

 neoclassical transport of impurities is strongly modified by its natural 

 poloidal distribution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articlee,

title = {Frontiers in Multiscale Modeling of Photoreceptor Proteins},

author = {Maria‐Andrea Mroginski and Suliman Adam and Gil Amoyal and Avishai Barnoy and Ana‐Nicoleta Bondar and Veniamin Borin and Jonathan Church and Tatiana Domratcheva and Bernd Ensing and Francesca Fanelli and Nicolas Ferré and Ofer Filiba and Laura Pedraza-González and Ronald González and Cristina González‐Espinoza and Rajiv Kar and Lukas Kemmler and Seung Kim and Jacob Kongsted and Igor Schapiro},

doi = {10.1111/php.13372},

year  = {2020},

date = {2020-01-01},

journal = {Photochemistry and Photobiology},

abstract = {This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modelling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green‐fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin are presented, along with methodological developments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articlef,

title = {Targeting Malaria Hotspots to Reduce Transmission Incidence in Senegal},

author = {Kankoé Sallah and Roch Giorgi and El-Hadj Ba and Martine Piarroux and Renaud Piarroux and Badara Cissé and Jean Gaudart},

doi = {10.3390/ijerph18010076},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Environmental Research and Public Health},

volume = {18},

pages = {76},

abstract = {In central Senegal, malaria incidence declined in response to scaling-up of control measures from 2000 to 2010 and has since remained stable, making elimination unlikely in the short term. Additional control measures are needed to reduce transmission. We simulated chemoprophylaxis interventions targeting malaria hotspots using a metapopulation mathematical model, based on a differential-equation framework and incorporating human mobility. The model was fitted to weekly malaria incidence from 45 villages. Three approaches for selecting intervention targets were compared: (a) villages with malaria cases during the low transmission season of the previous year; (b) villages with highest incidence during the high transmission season of the previous year; (c) villages with highest connectivity with adjacent populations. Our results showed that intervention strategies targeting hotspots would be effective in reducing malaria incidence in both targeted and untargeted areas. Regardless of the intervention strategy used, pre-elimination (1–5 cases per 1000 per year) would not be reached without simultaneously increasing vector control by more than 10%. A cornerstone of malaria control and elimination is the effective targeting of strategic locations. Mathematical tools help to identify those locations and estimate the impact in silico.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articleg,

title = {Predicting substitutions to modulate disorder and stability in coiled-coils},

author = {Yasaman Karami and Paul Saighi and Rémy Vanderhaegen and Denis Gerlier and Sonia Longhi and Elodie Laine and Alessandra Carbone},

doi = {10.1186/s12859-020-03867-x},

year  = {2020},

date = {2020-01-01},

journal = {BMC Bioinformatics},

volume = {21},

abstract = {Background Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function. However, characterizing their behaviour in solution and determining precisely the extent of disorder of a protein region remains challenging, both experimentally and computationally. Results In this work, we propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics (MD) simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV), both forming tetrameric left-handed coiled-coils. We show that our method can help quantify the extent of disorder of the C-terminus region of MeV and NiV PMDs from MD simulations of a few tens of nanoseconds, and without requiring an extensive exploration of the conformational space. Moreover, this study provided a conceptual framework for the rational design of substitutions aimed at modulating the stability of the coiled-coils. By assessing the impact of four substitutions known to destabilize coiled-coils, we derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. Conclusions Our method can be considered as a platform to reason about how to design substitutions aimed at regulating flexibility and stability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Boulet2020TheoreticalIO,

title = {Theoretical Investigations of the BaRh2Ge4X6 (X = S, Se, Te) Compounds},

author = {P Boulet and Marie-Christine Record},

url = {https://onlinelibrary.wiley.com/doi/10.1002/jccs.202000499},

year  = {2020},

date = {2020-01-01},

journal = {Energies},

volume = {13},

pages = {6434},

abstract = {The thermoelectric (TE) properties of the BaM2Ge4X6 compounds, where M = Rh and X = S, Se, Te, were investigated by computational approaches using density-functional theory and semi-classical Boltzmann theory for electronic transport. It was found that these compounds bear good TE properties, in particular BaRh2Ge4Te6, for which the figure of merit was estimated to reach 1.51 at 300 K. As this compound has not yet been proved to be stable, we also investigated BaRh2Ge4S4Te2 by assuming that replacing tellurium by sulphur could stabilize the tellurium-containing structure. It was found that the TE properties are good. The quantum theory of atoms in molecules was used to investigate the nature of the chemical interactions that prevail in these compounds. A wide variety of interactions were evidenced, from van der Waals interactions to ionic and polar-covalent ones, which could explain the good TE performance of these compounds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articleh,

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

author = {Shao-Long Guo and Yong-Liang Feng and Pierre Sagaut},

doi = {10.1063/5.0033364},

year  = {2020},

date = {2020-01-01},

journal = {Physics of Fluids},

volume = {32},

abstract = {Based on recent work by [Guo et. al, JCP,109570(2020)], an improved thermal hybrid recursive regularized lattice Boltzmann model (iHRR-ρ) on 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 Mach-temperature plane. An embedded hybridizing procedure is introduced in the quasi-symmetry correction terms, which allow for a decoupled treatment 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 in [Jacob et al, JoT,19,1151-1176(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 supersonic regime; III) non-isothermal acoustic pulse; IV) vortex-shock wave interaction; V) supersonic flow over NACA airfoil at Re=10000 and Ma=1.5; VI) compressible Taylor-Green vortex at Ma=0.29.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{renand:hal-02982205,

title = {Integrative molecular profiling of autoreactive CD4 T cells in autoimmune hepatitis},

author = {Amédée Renand and Iñaki Cervera-Marzal and Laurine Gil and Chuang Dong and Alexandra Garcia and Erwan Kervagoret and Hélène Aublé and Sarah Habes and Caroline Chevalier and Fabienne Vavasseur and Béatrice Clémenceau and Anaïs Cardon and Jean-Paul Judor and Jean-François Mosnier and Florence Tanné and David-Axel Laplaud and Sophie Brouard and Jérôme Gournay and Pierre Milpied and Sophie Conchon},

editor = {The Mw 6.5 Norcia earthquake occurred on 30 October 2016, along the Mt Vettore fault (Central Apennines, Italy), it was the largest earthquake of the 2016–2017 seismic sequence that started 2 months earlier with the Mw 6.0 Amatrice earthquake (24 August). To detect potential slow slip during the sequence, we produced Interferometric Synthetic Aperture Radar (InSAR) time series using 12‐ to 6‐day repeat cycles of Sentinel‐1A/1B images. Time series indicates that centimeter‐scale surface displacements took place during the 10 weeks following the Norcia earthquake. Two areas of subsidence are detected: one in the Castelluccio basin (hanging wall of the Mt Vettore fault) and one in the southern extent of the Norcia earthquake surface rupture, near an inherited thrust. Poroelastic and viscoelastic models are unable to explain these displacements. In the Castelluccio basin, the displacement reaches 13.2 ± 1.4 mm in the ascending line of sight on 6 January 2017. South of the Norcia earthquake surface rupture (a zone between the Norcia and Amatrice earthquakes), the postseismic surface displacements affect a smaller area but reach 35.5 ± 1.7 mm in ascending line of sight by January 2017 and follow a logarithmic temporal decay consistent with postseismic afterslip. Our analysis suggests that the structurally complex area located south of the Norcia rupture (30 October) is characterized by a conditionally stable frictional regime. This geometrical and frictional barrier likely halted rupture propagation during the Amatrice (24 August) and Norcia (30 October) earthquakes at shallow depth (<3–4 km).},

url = {https://hal.archives-ouvertes.fr/hal-02982205},

doi = {10.1016/j.jhep.2020.05.053},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Hepatology},

publisher = {Elsevier},

abstract = {Background & Aims:In most autoimmune disorders, crosstalk of B cells andCD4 T cells results in  the  accumulation  of  autoantibodies. In autoimmunehepatitis  (AIH),  the  presence  of  anti-Soluble Liver Antigen (SLA or SepSecs) autoantibodies is associated with significantly reduced overall  survival,  but  theassociatedautoreactive  CD4  T  cells  have  not  been  characterized  yet. Here we isolatedand deeply characterizedSLA-specific CD4 T cells in AIH patients.

Methods:We used brief ex vivorestimulation with overlapping SLA-derived peptidesto isolate and phenotype circulating SLA-specific CD4 T cells, and integrative single-cell RNA-seq (scRNA-seq)  to  characterize  their  transcriptome  and  TCR  repertoire  in  n=5  AIH  patients.SLA-specific CD4  T  cells  were  tracked  in  peripheral  blood  through  TCR  sequencing, to  identify  their phenotypic niche. We further characterized disease-associated peripheral blood T cells by high content  flow  cytometryin  an  additional  cohort  of  n=46  AIH  patients  and  n=18non-alcoholic steatohepatitis (NASH) controls.

Results:Autoreactive SLA-specific  CD4  T  cells were  only  detected  in  patients  with  anti-SLA autoantibodiesand  had  a  memory  PD-1+CXCR5-CCR6-CD27+phenotype. ScRNA-seq revealedtheirpro-inflammatory/B-Helper profile (IL21,  IFNG,  TIGIT,CTLA4,  NR3C1,  CD109, KLRB1andCLEC2D).Autoreactive TCR clonotypes were restricted to thememory PD-1+CXCR5-CD4 T cells. This  subset was  significantly  increased  in  the  blood  of  AIH  patients  and supported B  cell differentiationthrough     IL-21.Finally,     we identified a     specific     phenotype (PD-1+CD38+CD27+CD127-CXCR5-) of CD4 T cells linked to disease activity and IgG response during AIH. 

Conclusions:This  work provides for  the  first  time  a deep characterization  of  rare  circulating autoreactive  CD4  T  cells andtheidentification  oftheirperipheral  reservoir in  AIH.We  alsopropose a generic phenotype of pathogenic CD4 T cellsrelated toAIHdisease activity. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1029/2019JB019065,

title = {Localized Afterslip at Geometrical Complexities Revealed by InSAR After the 2016 Central Italy Seismic Sequence},

author = {Léa Pousse-Beltran and Anne Socquet and Lucilla Benedetti and Marie-Pierre Doin and Magali Rizza and Nicola D'Agostino},

url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JB019065},

doi = {https://doi.org/10.1029/2019JB019065},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Geophysical Research: Solid Earth},

volume = {125},

number = {11},

pages = {e2019JB019065},

abstract = {Abstract The Mw 6.5 Norcia earthquake occurred on 30 October 2016, along the Mt Vettore fault (Central Apennines, Italy), it was the largest earthquake of the 2016–2017 seismic sequence that started 2 months earlier with the Mw 6.0 Amatrice earthquake (24 August). To detect potential slow slip during the sequence, we produced Interferometric Synthetic Aperture Radar (InSAR) time series using 12- to 6-day repeat cycles of Sentinel-1A/1B images. Time series indicates that centimeter-scale surface displacements took place during the 10 weeks following the Norcia earthquake. Two areas of subsidence are detected: one in the Castelluccio basin (hanging wall of the Mt Vettore fault) and one in the southern extent of the Norcia earthquake surface rupture, near an inherited thrust. Poroelastic and viscoelastic models are unable to explain these displacements. In the Castelluccio basin, the displacement reaches 13.2 ± 1.4 mm in the ascending line of sight on 6 January 2017. South of the Norcia earthquake surface rupture (a zone between the Norcia and Amatrice earthquakes), the postseismic surface displacements affect a smaller area but reach 35.5 ± 1.7 mm in ascending line of sight by January 2017 and follow a logarithmic temporal decay consistent with postseismic afterslip. Our analysis suggests that the structurally complex area located south of the Norcia rupture (30 October) is characterized by a conditionally stable frictional regime. This geometrical and frictional barrier likely halted rupture propagation during the Amatrice (24 August) and Norcia (30 October) earthquakes at shallow depth (<3–4 km).},

note = {e2019JB019065 2019JB019065},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articlei,

title = {Thermoelectric Properties of Sb-S System Compounds from DFT Calculations},

author = {Hailong Yang and Pascal Boulet and Marie-Christine Record},

url = {https://www.mdpi.com/1996-1944/13/21/4707},

doi = {10.3390/ma13214707},

year  = {2020},

date = {2020-01-01},

journal = {Materials},

volume = {13},

number = {21},

pages = {4707},

abstract = {By combining density functional theory, quantum theory of atoms in molecules and transport properties calculations, we evaluated the thermoelectric properties of Sb-S system compounds and shed light on their relationships with electronic structures. The results show that, for Sb2S3, the large density of states (DOS) variation induces a large Seebeck coefficient. Taking into account the long-range weak bonds distribution, Sb2S3 should exhibit low lattice thermal conductivity. Therefore, Sb2S3 is promising for thermoelectric applications. The insertion of Be atoms into the Sb2S3 interstitial sites demonstrates the electrical properties and Seebeck coefficient anisotropy and sheds light on the understanding of the role of quasi-one-dimensional structure in the electron transport. The large interstitial sites existing in SbS2 are at the origin of phonons anharmonicity which counteracts the thermal transport. The introduction of Zn and Ga atoms into these interstitial sites could result in an enhancement of all the thermoelectric properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1162/neco_a_01325,

title = {Effect of Top-Down Connections in Hierarchical Sparse Coding},

author = {Victor Boutin and Angelo Franciosini and Franck Ruffier and Laurent Perrinet},

url = {https://doi.org/10.1162/neco_a_01325},

doi = {10.1162/neco_a_01325},

year  = {2020},

date = {2020-01-01},

journal = {Neural Computation},

volume = {32},

number = {11},

pages = {2279-2309},

abstract = {Hierarchical sparse coding (HSC) is a powerful model to efficiently represent multidimensional, structured data such as images. The simplest solution to solve this computationally hard problem is to decompose it into independent layer-wise subproblems. However, neuroscientific evidence would suggest interconnecting these subproblems as in predictive coding (PC) theory, which adds top-down connections between consecutive layers. In this study, we introduce a new model, 2-layer sparse predictive coding (2L-SPC), to assess the impact of this interlayer feedback connection. In particular, the 2L-SPC is compared with a hierarchical Lasso (Hi-La) network made out of a sequence of independent Lasso layers. The 2L-SPC and a 2-layer Hi-La networks are trained on four different databases and with different sparsity parameters on each layer. First, we show that the overall prediction error generated by 2L-SPC is lower thanks to the feedback mechanism as it transfers prediction error between layers. Second, we demonstrate that the inference stage of the 2L-SPC is faster to converge and generates a refined representation in the second layer compared to the Hi-La model. Third, we show that the 2L-SPC top-down connection accelerates the learning process of the HSC problem. Finally, the analysis of the emerging dictionaries shows that the 2L-SPC features are more generic and present a larger spatial extension.},

note = {PMID: 32946716},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1162/neco_a_01325b,

title = {Correcting inaccurate background mortality in excess hazard models through breakpoints},

author = {Robert Darlin Mba and Juste Aristide Goungounga and Nathalie Graffeo and Roch Giorgi},

url = {https://www.hal.inserm.fr/inserm-03104366},

doi = {10.1186/s12874-020-01139-z},

year  = {2020},

date = {2020-01-01},

journal = {BMC Medical Research Methodology},

volume = {20},

number = {1},

pages = {268},

publisher = {BioMed Central},

abstract = {Methods for estimating relative survival are widely used in population-based cancer survival studies. These methods are based on splitting the observed (the overall) mortality into excess mortality (due to cancer) and background mortality (due to other causes, as expected in the general population). The latter is derived from life tables usually stratified by age, sex, and calendar year but not by other covariates (such as the deprivation level or the socioeconomic status) which may lack though they would influence background mortality. The absence of these covariates leads to inaccurate background mortality, thus to biases in estimating the excess mortality. These biases may be avoided by adjusting the background mortality for these covariates whenever available.Methods for estimating relative survival are widely used in population-based cancer survival studies. These methods are based on splitting the observed (the overall) mortality into excess mortality (due to cancer) and background mortality (due to other causes, as expected in the general population). The latter is derived from life tables usually stratified by age, sex, and calendar year but not by other covariates (such as the deprivation level or the socioeconomic status) which may lack though they would influence background mortality. The absence of these covariates leads to inaccurate background mortality, thus to biases in estimating the excess mortality. These biases may be avoided by adjusting the background mortality for these covariates whenever available.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ZHANG2020120174,

title = {An extensive numerical study of the burning dynamics of wildland fuel using proposed configuration space},

author = {Kai Zhang and Aymeric Lamorlette},

url = {https://www.sciencedirect.com/science/article/pii/S0017931020331100},

doi = {https://doi.org/10.1016/j.ijheatmasstransfer.2020.120174},

issn = {0017-9310},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Heat and Mass Transfer},

volume = {160},

pages = {120174},

abstract = {Physics-based flame models capable of predicting small-scale fire behaviors reduce computational power needed for predicting fires of large- and giga-scale. However, classical model correlations are often developed for ‘free fires’ without considering vegetation around. These models may result in inaccurate fire modeling due to wrong ‘prior’ flame shape estimated from θ ~ wind speed. To overcome this defect, three-dimensional small-scale fires with fireline intensity of 100 KW/m are numerically simulated using large eddy simulation. Fire behaviors such as flame tilt angle and heat transfer mechanisms are extensively studied using a newly proposed configuration space NC, CdLAI. The former one represents the ratio between fire to wind power, and the latter one considering the vegetation effect is for the first time introduced in flame models. Using the configuration space, two model correlations for flame tilt angle and radiative heat power reaching the unburnt fuels are proposed. The flame tilt angle θ is directly related to CdLAI (CdαsσsHF/2), while inversely related to NC (2gI/ρ0Cp,0T0U03), in contrast to the model proposed for radiative heat power. Comparisons with several classical models evidenced the capability of new flame models in predicting both free and non-free fires. The limits of the validity of the newly proposed models are also discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GUO2020109570,

title = {An efficient lattice Boltzmann method for compressible aerodynamics on D3Q19 lattice},

author = {S Guo and Y Feng and J Jacob and F Renard and P Sagaut},

url = {https://www.sciencedirect.com/science/article/pii/S0021999120303442},

doi = {https://doi.org/10.1016/j.jcp.2020.109570},

issn = {0021-9991},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Computational Physics},

volume = {418},

pages = {109570},

abstract = {An efficient lattice Boltzmann (LB) model relying on a hybrid recursive regularization (HRR) collision operator on D3Q19 stencil is proposed for the simulation of three-dimensional high-speed compressible flows in both subsonic and supersonic regimes. An improved thermal equilibrium distribution function on D3Q19 lattice is derived to reduce the complexity of correcting terms. A simple shock capturing scheme and an upwind biased discretization of correction terms are implemented for supersonic flows with shocks. Mass and momentum equations are recovered by an efficient streaming, collision and forcing process on D3Q19 lattice. Then a non-conservative formulation of the entropy evolution equation is used, that is solved using a finite volume method. The proposed method is assessed considering the simulation of i) 2D isentropic vortex convection, ii) 3D non-isothermal acoustic pulse, iii) 2D supersonic flow over a bump, iv) 3D shock explosion in a box, v) 2D vortex interaction with shock wave, vi) 2D laminar flows over a flat plate at Ma of 0.5, 1.0 and 1.5.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{D0SC04197A,

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

author = {Fábris Kossoski and Mario Barbatti},

url = {http://dx.doi.org/10.1039/D0SC04197A},

doi = {10.1039/D0SC04197A},

year  = {2020},

date = {2020-01-01},

journal = {Chem. Sci.},

volume = {11},

pages = {9827-9835},

publisher = {The Royal Society of Chemistry},

abstract = {Despite the continuous development of theoretical methodologies for describing nonadiabatic dynamics of molecular systems, there is a lack of approaches for processes where the norm of the wave function is not conserved, i.e., when an imaginary potential accounts for some irreversible decaying mechanism. Current approaches rely on building potential energy surfaces of reduced dimensionality, which is not optimal for more involving and realistic multidimensional problems. Here, we present a novel methodology for describing the dynamics of complex-valued molecular Hamiltonians, which is a generalisation of the trajectory surface hopping method. As a first application, the complex surface fewest switches surface hopping (CS-FSSH) method was employed to survey the relaxation mechanisms of the shape resonant anions of iodoethene. We have provided the first detailed and dynamical picture of the π*/σ* mechanism of dissociative electron attachment in halogenated unsaturated compounds, which is believed to underlie electron-induced reactions of several molecules of interest. Electron capture into the π* orbital promotes CC stretching and out-of-plane vibrations, followed by charge transfer from the double bond into the σ* orbital at the C–I bond, and, finally, release of the iodine ion, all within only 15 fs. On-the-fly dynamics simulations of a vast class of processes can be envisioned with the CS-FSSH methodology, including autoionisation from transient anions, core-ionised and superexcited states, Auger and interatomic coulombic decay, and time-dependent luminescence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ouyang:hal-02959804,

title = {Absolute configuration and host-guest binding of chiral porphyrin-cages by a combined chiroptical and theoretical approach},

author = {Jiangkun Ouyang and Anne Swartjes and Marc Geerts and Pieter J Gilissen and D Wang and Paula C P Teeuwen and paul Tinnemans and Nicolas Vanthuyne and Sara Chentouf and Floris P J T Rutjes and J -V Naubron and Jeanne Crassous and Johannes A A W Elemans and R Nolte},

url = {https://hal.archives-ouvertes.fr/hal-02959804},

doi = {10.1038/s41467-020-18596-1},

year  = {2020},

date = {2020-01-01},

journal = {Nature Communications},

volume = {11},

number = {1},

pages = {4776},

publisher = {Nature Publishing Group},

abstract = {Porphyrin cage-compounds are used as biomimetic models and substrate-selective catalysts in supramolecular chemistry. In this work we present the resolution of planar-chiral porphyrin cages and the determination of their absolute configuration by vibrational circular dichroism in combination with density functional theory calculations. The chiral porphyrin-cages form complexes with achiral and chiral viologen-guests and upon binding one of the axial enantiomorphs of the guest is bound selectively, as is indicated by induced-electronic-dichroism-spectra in combination with calculations. This host-guest binding also leads to unusual enhanced vibrational circular dichroism, which is the result of a combination of phenomena, such as rigidification of the host and guest structures, charge transfer, and coupling of specific vibration modes of the host and guest. The results offer insights in how the porphyrin cage-compounds may be used to construct a future molecular Turing machine that can write chiral information onto polymer chains.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GIORGIANI2020107375,

title = {A high-order non field-aligned approach for the discretization of strongly anisotropic diffusion operators in magnetic fusion},

author = {G Giorgiani and H Bufferand and F Schwander and E Serre and P Tamain},

url = {https://www.sciencedirect.com/science/article/pii/S0010465520301612},

doi = {https://doi.org/10.1016/j.cpc.2020.107375},

issn = {0010-4655},

year  = {2020},

date = {2020-01-01},

journal = {Computer Physics Communications},

volume = {254},

pages = {107375},

abstract = {In this work we present a hybrid discontinuous Galerkin scheme for the solution of extremely anisotropic diffusion problems arising in magnetized plasmas for fusion applications. Unstructured meshes, non-aligned with respect to the dominant diffusion direction, allow an unequalled flexibility in discretizing geometries of any shape, but may lead to spurious numerical diffusion. Curved triangles or quadrangles are used to discretize the poloidal plane of the machine, while a structured discretization is used in the toroidal direction. The proper design of the numerical fluxes guarantees the correct convergence order at any anisotropy level. Computations performed on well-designed 2D and 3D numerical tests show that non-aligned discretizations are able to provide spurious diffusion free solutions as long as high-order interpolations are used. Introducing an explicit measure of the numerical diffusion, a careful investigation is carried out showing an exponential increase of this latest with respect to the non-alignment of the mesh with the diffusion direction, as well as an exponential decrease with the polynomial degree of interpolation. A brief assessment of the method with respect to two finite-difference schemes using non-aligned discretization, but classically used in fusion modeling, is also presented. 

Program summary 

Program Title: Laplace-HDG (Laplace Hybrid Discontinuous Galerkin) CPC Library link to program files: http://dx.doi.org/10.17632/c3dhycyvj8.1 Licensing provisions: GPLv3 Programming language: Fortran 95 Nature of problem: Anisotropic Laplace problem in 2D with Dirichlet boundary conditions Solution method: Hybrid discontinuous Galerkin scheme},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{GIORGIANI2020107375b,

title = {A high-order non field-aligned approach for the discretization of strongly anisotropic diffusion operators in magnetic fusion},

author = {G Giorgiani and H Bufferand and F Schwander and E Serre and P Tamain},

url = {https://www.sciencedirect.com/science/article/pii/S0010465520301612},

doi = {https://doi.org/10.1016/j.cpc.2020.107375},

issn = {0010-4655},

year  = {2020},

date = {2020-01-01},

journal = {Computer Physics Communications},

volume = {254},

pages = {107375},

abstract = {In this work we present a hybrid discontinuous Galerkin scheme for the solution of extremely anisotropic diffusion problems arising in magnetized plasmas for fusion applications. Unstructured meshes, non-aligned with respect to the dominant diffusion direction, allow an unequalled flexibility in discretizing geometries of any shape, but may lead to spurious numerical diffusion. Curved triangles or quadrangles are used to discretize the poloidal plane of the machine, while a structured discretization is used in the toroidal direction. The proper design of the numerical fluxes guarantees the correct convergence order at any anisotropy level. Computations performed on well-designed 2D and 3D numerical tests show that non-aligned discretizations are able to provide spurious diffusion free solutions as long as high-order interpolations are used. Introducing an explicit measure of the numerical diffusion, a careful investigation is carried out showing an exponential increase of this latest with respect to the non-alignment of the mesh with the diffusion direction, as well as an exponential decrease with the polynomial degree of interpolation. A brief assessment of the method with respect to two finite-difference schemes using non-aligned discretization, but classically used in fusion modeling, is also presented. 

Program summary 

Program Title: Laplace-HDG (Laplace Hybrid Discontinuous Galerkin) CPC Library link to program files: http://dx.doi.org/10.17632/c3dhycyvj8.1 Licensing provisions: GPLv3 Programming language: Fortran 95 Nature of problem: Anisotropic Laplace problem in 2D with Dirichlet boundary conditions Solution method: Hybrid discontinuous Galerkin scheme},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DENG2020405,

title = {Diffuse interface modelling of reactive multi-phase flows applied to a sub-critical cryogenic jet},

author = {Xi Deng and Pierre Boivin},

url = {https://www.sciencedirect.com/science/article/pii/S0307904X20301943},

doi = {https://doi.org/10.1016/j.apm.2020.04.011},

issn = {0307-904X},

year  = {2020},

date = {2020-01-01},

journal = {Applied Mathematical Modelling},

volume = {84},

pages = {405-424},

abstract = {In order to simulate cryogenic H2−O2 jets under subcritical condition, a numerical model is constructed to solve compressible reactive multi-component flows which involve complex multi-physics processes such as moving material interfaces, shock waves, phase transition and combustion. The liquid and reactive gaseous mixture are described by a homogeneous mixture model with diffusion transport for heat, momentum and species. A hybrid thermodynamic closure strategy is proposed to construct an equation of state (EOS) for the mixture. The phase transition process is modeled by a recent fast relaxation method which gradually reaches the thermo-chemical equilibrium without iterative process. A simplified transport model is also implemented to ensure the accurate behavior in the limit of pure fluids and maintain computational efficiency. Last, a 12-step chemistry model is included to account for hydrogen combustion. Then the developed numerical model is solved with the finite volume method where a low dissipation AUSM (advection upstream splitting method) Riemann solver is extended for multi-component flows. A homogeneous reconstruction strategy compatible with the homogeneous mixture model is adopted to prevent numerical oscillations across material interfaces. Having included these elements, the model is validated on a number of canonical configurations, first for multiphase flows, and second for reactive flows. These tests allow recovery of the expected behavior in both the multiphase and reactive limits, and the model capability is further demonstrated on a 2D burning cryogenic H2−O2 jet, in a configuration reminiscent of rocket engine ignition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/anie.202003504,

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},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202003504},

doi = {https://doi.org/10.1002/anie.202003504},

year  = {2020},

date = {2020-01-01},

journal = {Angewandte Chemie International Edition},

volume = {59},

number = {37},

pages = {16233-16240},

abstract = {Abstract We 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{mizuno:hal-02871575,

title = {Numerical and Experimental Study of Wave Propagation in Water-Saturated Granular Media Using Effective Method Theories and a Full-Wave Numerical Simulation},

author = {Katsunori Mizuno and Paul Cristini and Dimitri Komatitsch and Yann Capdeville},

url = {https://hal.archives-ouvertes.fr/hal-02871575},

doi = {10.1109/JOE.2020.2983865},

year  = {2020},

date = {2020-01-01},

journal = {IEEE Journal of Oceanic Engineering},

volume = {45},

number = {3},

pages = {772 - 785},

publisher = {Institute of Electrical and Electronics Engineers},

abstract = {In this article, the detection of an object buried in marine sediments is investigated. Using the results from a series of experiments realized in a tank filled with water and calibrated glass beads, we evaluate the performances for a wide range of the value of the ratio kd of the grain size to the wavelength (k is the wave number and d is the grain diameter) of three types of prediction tools. The first two prediction tools are based on the definition of an equivalent model. The first tool is based on the well-known Biot-Stoll theory (BM model) while the second tool uses nonperiodic homogenization to define effective velocity and anisotropy maps representing the medium (HM model). The last prediction tool implements a time-domain full-wave numerical method, which takes into account each grain separately (GM model). It is shown that a good agreement between experiments and numerical simulations can be achieved using the BM model for the low kd regime and the HM model for high kd regime. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{feng:hal-02892273,

title = {Grid refinement in the three-dimensional hybrid recursive regularized lattice Boltzmann method for compressible aerodynamics},

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

url = {https://hal.archives-ouvertes.fr/hal-02892273},

doi = {10.1103/PhysRevE.101.063302},

year  = {2020},

date = {2020-01-01},

journal = {Physical Review E },

volume = {101},

number = {6},

pages = {063302},

publisher = {American Physical Society (APS)},

abstract = {Grid refinement techniques are of paramount importance for computational fluid dynamics approaches relying on the use of Cartesian grids. This is especially true of solvers dedicated to aerodynamics, in which the capture of thin shear layers require the use of small cells. In this paper, a three-dimensional grid refinement technique is developed within the framework of hybrid recursive regularized lattice Boltzmann method (HRR-LBM) for compressible high-speed flows, which is an efficient collide-stream-type method on a compact D3Q19 stencil. The proposed method is successfully assessed considering several test cases, namely, an isentropic vortex propagating through transition interface, shock-vortex interaction with intersection between grid refinement interface and shock corrugation, and transonic flows over three-dimensional DLR-M6 wing with seven levels of grid refinement. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{YANG2020121266,

title = {New insight into the structure-property relationships from chemical bonding analysis: Application to thermoelectric materials},

author = {Hailong Yang and Pascal Boulet and Marie-Christine Record},

url = {https://www.sciencedirect.com/science/article/pii/S0022459620300967},

doi = {https://doi.org/10.1016/j.jssc.2020.121266},

issn = {0022-4596},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Solid State Chemistry},

volume = {286},

pages = {121266},

abstract = {Structure-property relationships are indisputably important to deeply understand the nature of materials. The main direction pursued to investigate these relations is based on the chemical bonding concept. The integral and local properties of chemical bonding determined from the topological analysis of electron density by combining the quantum theory of atoms in molecules (AIM) and DFT calculations can aid to build a bridge between the atomic structure and the intrinsic properties of materials. In this paper, the electronic and thermal transport properties of thermoelectric materials in the Cu–Sb–Se system have been analysed by coupling energy densities relationships and corresponding electron density Laplacian distribution for specific interactions. The asset of this method is to directly highlight the influence of lone pair electrons and atomic fluctuations on interatomic interactions as well as the coupling effect of weak bonds, which offers a new approach to design and search for materials with low thermal conductivity at low calculation cost.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{YANG2020112784,

title = {A rapid method for analyzing the chemical bond from energy densities calculations at the bond critical point},

author = {Hailong Yang and Pascal Boulet and Marie-Christine Record},

url = {https://www.sciencedirect.com/science/article/pii/S2210271X20300840},

doi = {https://doi.org/10.1016/j.comptc.2020.112784},

issn = {2210-271X},

year  = {2020},

date = {2020-01-01},

journal = {Computational and Theoretical Chemistry},

volume = {1178},

pages = {112784},

abstract = {The quantum theory atoms in molecules (QTAIM) method has been used in this paper to characterize various bonding interactions in molecules and solid compounds. By using DFT-PAW calculations, complete electron density Laplacian distributions have been obtained and related to energies densities calculated at the bond critical points. From the analysis of these results a simple and rapid method, based solely on local energies densities calculations, is proposed to diagnose the bonding state, the polarizability and the deformation of the charge distribution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cartiermichaud:hal-02613800,

title = {A posteriori error estimate in fluid simulations of turbulent edge plasmas for magnetic fusion in tokamak using the data mining iPoPe method},

author = {T Cartier-Michaud and D Galassi and Ph Ghendrih and P Tamain and F Schwander and E Serre},

url = {https://hal.archives-ouvertes.fr/hal-02613800},

year  = {2020},

date = {2020-01-01},

journal = {Physics of Plasmas},

publisher = {American Institute of Physics},

abstract = {Progressing towards more reliable numerical solutions in the simulation of plasma for magnetic confinement fusion has become a critical issue for the success of the ITER operation. This requires developing rigorous and efficient methods of verification of the numerical simulations in any relevant flow regimes of the operation. The paper introduces a new formulation of the PoPe 1 method, namely the independent Projection on Proper elements method (iPoPe) to quantify the numerical error by performing a data-driven identification of the mathematical model from the simulation outputs. Based on a statistical postprocessing of the outputs database, the method provides a measure of the error by estimating the distance between the (numerical) effective and (analytical) theoretical weights of each operator implemented in the mathematical model. The efficiency of the present method is illustrated on turbulent edge plasma simulations based on a drift-reduced Braginskii fluid model in realistic magnetic geometries. Results show the effective order of the numerical method in these multiscale flow regimes as well as the values of the plasma parameters which can be safely simulated with respect to a given discretization. In this sense, the method goes one step further than the Method of Manufactured Solution (MMS 2-4), recently introduced in fusion, and provides an efficient verification procedure of the numerical simulations in any regimes, including turbulent ones that could be generalized to other scientific domains. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{siddique:hal-02612347,

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

author = {Farhan Siddique and Mario Barbatti and Zhonghua Cui and Hans Lischka and Adélia Aquino},

url = {https://hal-amu.archives-ouvertes.fr/hal-02612347},

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

year  = {2020},

date = {2020-01-01},

journal = {Journal of Physical Chemistry A},

volume = {124},

number = {17},

pages = {3347-3357},

publisher = {American Chemical Society},

abstract = {Surface hopping quantum mechanical/molecular dynamics simulations have been performed for the tetracyanoethylene–anthracene complex to investigate the evolution of charge-transfer (CT) states after excitation into a locally excited (LE) state of anthracene. The scaled opposite-spin (SOS) second-order algebraic diagrammatic construction (SOS-ADC(2)) has been used to achieve a balanced description of LE and CT states. The calculations have been performed for two media, the gas phase and water (described by molecular mechanics, MM). The two dynamics variants show strongly different behaviors. Even though in both cases the conversion from the LE state to lower-lying CT states occurs with 100 fs, in the gas phase, the system remains in the excited state for longer than 2 ps, while in water, it returns to the ground state within 0.5 ps. Moreover, while in the gas phase the original neutral equilibrium structure should be recovered, in water, the ion-pair (IPr) CT state is strongly stabilized, creating a new competing ground-state isomer. Thus, we predict that the ground state of the complex in water should be composed of two species, the original neutral state and an IPr state. The existence of an IPr ground state in strongly polar environments opens interesting possibilities for the design of efficient charge-separating organic donor–acceptor interfaces. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bai:hal-02612358,

title = {On the Origin of the Shift Between Vertical Excitation and Band Maximum in Molecular Photoabsorption},

author = {Shuming Bai and Ritam Mansour and Ljiljana Stojanovi{'c} and Josene Toldo and Mario Barbatti},

url = {https://hal-amu.archives-ouvertes.fr/hal-02612358},

doi = {10.1007/s00894-020-04355-y},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Molecular Modeling},

volume = {26},

number = {5},

publisher = {Springer Verlag (Germany)},

abstract = {The analysis of the photoabsorption spectra of molecules shows that the band maximum is usually redshifted in comparison to the vertical excitation. We conducted a throughout analysis of this shift based on low-dimensional analytical and numerical model systems, showing that its origin is rooted in the frequency changing between the ground and the excited states in multidimensional systems. Moreover, we deliver a benchmark of ab initio results for the shift based on a comparison of vertical excitations and band maxima calculated with the nuclear ensemble approach for the 28 organic molecules in the Mülheim molecular dataset. The mean value of the shift calculated over 60 transitions is 0.11 ± 0.08 eV. The mean value of the band width is 0.32 ± 0.14 eV. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{D0TC00131G,

title = {First-principles calculations on CuInSe2/AlP heterostructures},

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

url = {http://dx.doi.org/10.1039/D0TC00131G},

doi = {10.1039/D0TC00131G},

year  = {2020},

date = {2020-01-01},

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

volume = {8},

pages = {4732-4742},

publisher = {The Royal Society of Chemistry},

abstract = {Heterostructures based on a CuInSe2 absorber with an AlP buffer have been modeled for the first time using different stacking schemes and interfacial terminations. Mechanical, electronic and topological properties of CuInSe2/AlP heterostructures along the [001] direction were investigated using the full potential linear augmented plane wave (FP-LAPW) method. Optimal interfacial distance, thermodynamic stability and band alignment have been computed systematically. A heterointerface with “on-top” stacking is thermodynamically the most stable compared with other stackings. The magnitudes of core level binding energy differences are in accordance with interfacial adhesion energies. Absolute deformation potentials (ADPs) of band energies as a function of (001) biaxial strain were determined. With redressing of ADPs, the revised valence and conduction band offsets have increased and decreased, respectively. AlP has strong resistance to biaxial strain in the evolution of band energy edges. Topological properties and density of states were used to investigate the relationship between interatomic interactions and energy band evolution. The most stable CuInSe2/AlP heterostructures have “spike-like” band offsets, with the one terminated as Se–Al characterized by a flat conduction band offset of 12 meV. This comes from the strong “Cu d-Se p” states hybridization. The theoretical maximum conversion efficiency of the AlP-based “absorber-buffer” heterostructure is 27.39% at 0.5 μm thickness.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articlej,

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

author = {Hans Lischka and Ron Shepard and Thomas Mueller and Péter Szalay and Russell Pitzer and Adélia Aquino and Mayzza Nascimento and Mario Barbatti and Lachlan Belcher and Jean Blaudeau and Itamar Jr and Scott Brozell and Emily Carter and Anita Das and Gergely Gidofalvi and Leticia González and William Hase and Gary Kedziora and Miklos Kertesz and Zhiyong Zhang},

doi = {10.1063/1.5144267},

year  = {2020},

date = {2020-01-01},

journal = {The Journal of Chemical Physics},

volume = {152},

pages = {134110},

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{BENSEGHIER2020103404,

title = {A parallel GPU-based computational framework for the micromechanical analysis of geotechnical and erosion problems},

author = {Zeyd Benseghier and Pablo Cuéllar and Li-Hua Luu and Stéphane Bonelli and Pierre Philippe},

url = {https://www.sciencedirect.com/science/article/pii/S0266352X19304689},

doi = {https://doi.org/10.1016/j.compgeo.2019.103404},

issn = {0266-352X},

year  = {2020},

date = {2020-01-01},

journal = {Computers and Geotechnics},

volume = {120},

pages = {103404},

abstract = {This article deals with the relevance and practical feasibility of micromechanical simulations for their application to general geomechanical problems involving fluid-saturated granular assemblies, whether frictional or cohesive. A set of conceptual and numerical tools is here presented, advocating for a parallel computation using graphical processing units (GPUs) to treat large numbers of degrees of freedom with conventional desktop computers. The fluid phase is here simulated with a particle-resolved approach in the frame of the Lattice Botzmann Method (LBM) while the granular solid phase is modelled as a collection of discrete particles from a Molecular Dynamics DEM perspective. The range of possible material behaviours for the solid granular phase is intended here to cover a broad spectrum from purely frictional to viscous cohesive materials with either brittle or transient debonding features. Specific details of the implementation and some validation cases are put forward. Finally, some exemplary applications in the fields of soil erosion and geotechnical profile installation are provided along with a discussion on the parallel performance of the presented models. The results show that a micromechanical approach can be feasible and useful in practice, providing meaningful insights into complex engineering problems like the erosion kinetics of a soil under an impinging jet or the penetration resistance of a deep foundation in a layered soil profile.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{TRUONG2020104426,

title = {A mass-spring fluid-structure interaction solver: Application to flexible revolving wings},

author = {Hung Truong and Thomas Engels and Dmitry Kolomenskiy and Kai Schneider},

url = {https://www.sciencedirect.com/science/article/pii/S0045793020300025},

doi = {https://doi.org/10.1016/j.compfluid.2020.104426},

issn = {0045-7930},

year  = {2020},

date = {2020-01-01},

journal = {Computers & Fluids},

volume = {200},

pages = {104426},

abstract = {The secret to the spectacular flight capabilities of flapping insects lies in their wings, which are often approximated as flat, rigid plates. Real wings are however delicate structures, composed of veins and membranes, and can undergo significant deformation. In the present work, we present detailed numerical simulations of such deformable wings. Our results are obtained with a fluid–structure interaction solver, coupling a mass–spring model for the flexible wing with a pseudo-spectral code solving the incompressible Navier–Stokes equations. We impose the no-slip boundary condition through the volume penalization method; the time-dependent complex geometry is then completely described by a mask function. This allows solving the governing equations of the fluid on a regular Cartesian grid. Our implementation for massively parallel computers allows us to perform high resolution computations with up to 500 million grid points. The mass–spring model uses a functional approach, thus modeling the different mechanical behaviors of the veins and the membranes of the wing. We perform a series of numerical simulations of a flexible revolving bumblebee wing at a Reynolds number Re=1800. In order to assess the influence of wing flexibility on the aerodynamics, we vary the elasticity parameters and study rigid, flexible and highly flexible wing models. Code validation is carried out by computing classical benchmarks.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articlek,

title = {Three-dimensional wing structure attenuates aerodynamic efficiency in flapping fly wings},

author = {Thomas Engels and Henja-Niniane Wehmann and Fritz-Olaf Lehmann},

doi = {10.1098/rsif.2019.0804},

year  = {2020},

date = {2020-01-01},

journal = {Journal of The Royal Society Interface},

volume = {17},

pages = {20190804},

abstract = {The aerial performance of flying insects ultimately depends on how flapping wings interact with the surrounding air. It has previously been suggested that the wing's three-dimensional camber and corrugation help to stiffen the wing against aerodynamic and inertial loading during flapping motion. Their contribution to aerodynamic force production, however, is under debate. Here, we investigated the potential benefit of three-dimensional wing shape in three different-sized species of flies using models of micro-computed tomography-scanned natural wings and models in which we removed either the wing's camber, corrugation, or both properties. Forces and aerodynamic power requirements during root flapping were derived from three-dimensional computational fluid dynamics modelling. Our data show that three-dimensional camber has no benefit for lift production and attenuates Rankine–Froude flight efficiency by up to approximately 12% compared to a flat wing. Moreover, we did not find evidence for lift-enhancing trapped vortices in corrugation valleys at Reynolds numbers between 137 and 1623. We found, however, that in all tested insect species, aerodynamic pressure distribution during flapping is closely aligned to the wing's venation pattern. Altogether, our study strongly supports the assumption that the wing's three-dimensional structure provides mechanical support against external forces rather than improving lift or saving energetic costs associated with active wing flapping.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articlel,

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},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Immunology},

volume = {11},

pages = {2047},

abstract = {The aerial performance of flying insects ultimately depends on how flapping wings interact with the surrounding air. It has previously been suggested that the wing's three-dimensional camber and corrugation help to stiffen the wing against aerodynamic and inertial loading during flapping motion. Their contribution to aerodynamic force production, however, is under debate. Here, we investigated the potential benefit of three-dimensional wing shape in three different-sized species of flies using models of micro-computed tomography-scanned natural wings and models in which we removed either the wing's camber, corrugation, or both properties. Forces and aerodynamic power requirements during root flapping were derived from three-dimensional computational fluid dynamics modelling. Our data show that three-dimensional camber has no benefit for lift production and attenuates Rankine–Froude flight efficiency by up to approximately 12% compared to a flat wing. Moreover, we did not find evidence for lift-enhancing trapped vortices in corrugation valleys at Reynolds numbers between 137 and 1623. We found, however, that in all tested insect species, aerodynamic pressure distribution during flapping is closely aligned to the wing's venation pattern. Altogether, our study strongly supports the assumption that the wing's three-dimensional structure provides mechanical support against external forces rather than improving lift or saving energetic costs associated with active wing flapping.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ZHANG2020102950,

title = {A study of the canopy effect on fire regime transition using an objectively defined Byram convective number},

author = {Kai Zhang and Salman Verma and Arnaud Trouvé and Aymeric Lamorlette},

url = {https://www.sciencedirect.com/science/article/pii/S0379711219304497},

doi = {https://doi.org/10.1016/j.firesaf.2020.102950},

issn = {0379-7112},

year  = {2020},

date = {2020-01-01},

journal = {Fire Safety Journal},

volume = {112},

pages = {102950},

abstract = {Forest fires can be classified into two regimes, depending on Byram convective number NC: a plume-dominated and wind-driven regime. This classification is often based on two-dimensional (2D) studies without considering flame front structures, and is associated with the change of governing heat transfer mechanism. Studies based on three-dimensional (3D) considerations suggest the dependency of the fire regime transition on canopy characteristics CdLAI (CdαsσsHF/2) through which the atmosphere boundary layer (ABL) flow changes to mixing layer (ML) flow. Hence, the primary objective of the present study is to investigate the fire regime transition and its associated heat transfer mechanisms with the aid of drawing a dimensionless configuration space NC, CdLAI. This requires an objective definition of the Byram convective number; the 2 m or 10 m high open wind speed (U∞=U2 or U10) often used to define it being arbitrary. Therefore, the present study introduces a scaling method for the reference height (Yref) at which the wind speed Uref is chosen to define a new Byram convective number NC’. A mathematical expression for Yref as a function of canopy/vegetation height is proposed for a small-scale, stationary fire. The new configuration space NC’, CdLAI is considered more suitable for investigating the fire regime transition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/gji/ggaa456,

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},

url = {https://doi.org/10.1093/gji/ggaa456},

doi = {10.1093/gji/ggaa456},

issn = {0956-540X},

year  = {2020},

date = {2020-01-01},

journal = {Geophysical Journal International},

volume = {224},

number = {1},

pages = {719-737},

abstract = {It 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{articlec,

title = {Efficiency of laminar and turbulent mixing in wall-bounded flows},

author = {Benjamin Kadoch and Wouter Bos and Kai Schneider},

doi = {10.1103/PhysRevE.101.043104},

year  = {2020},

date = {2020-01-01},

journal = {Physical Review E},

volume = {101},

abstract = {A turbulent flow mixes in general more rapidly a passive scalar than a laminar flow does. From an energetic point of view, for statistically homogeneous or periodic flows, the laminar regime is more efficient. However, the presence of walls may change this picture. We consider in this investigation mixing in two-dimensional laminar and turbulent wall-bounded flows using direct numerical simulation. We show that for sufficiently large Schmidt number, turbulent flows more efficiently mix a wall-bounded scalar field than a chaotic or laminar flow does. The mixing efficiency is shown to be a function of the Péclet number, and a phenomenological explanation yields a scaling law, consistent with the observations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{favier_knobloch_2020,

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

author = {Benjamin Favier and Edgar Knobloch},

doi = {10.1017/jfm.2020.310},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Fluid Mechanics},

volume = {895},

pages = {R1},

publisher = {Cambridge University Press},

abstract = {We show, using direct numerical simulations with experimentally realizable boundary conditions, that wall modes in Rayleigh–Bénard convection in a rapidly rotating cylinder persist even very far from their linear onset. These nonlinear wall states survive in the presence of turbulence in the bulk and are robust with respect to changes in the shape of the boundary of the container. In this sense, these states behave much like the topologically protected states present in two-dimensional chiral systems even though rotating convection is a three-dimensional nonlinear driven dissipative system. We suggest that the robustness of this nonlinear state may provide an explanation for the strong zonal flows observed recently in experiments and simulations of rapidly rotating convection at high Rayleigh number.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{D0CP01714K,

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},

url = {http://dx.doi.org/10.1039/D0CP01714K},

doi = {10.1039/D0CP01714K},

year  = {2020},

date = {2020-01-01},

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

volume = {22},

pages = {12447-12455},

publisher = {The Royal Society of Chemistry},

abstract = {Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1021/acs.jctc.9b01145,

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},

url = {https://doi.org/10.1021/acs.jctc.9b01145},

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

year  = {2020},

date = {2020-01-01},

journal = {Journal of Chemical Theory and Computation},

volume = {16},

number = {6},

pages = {3816-3824},

abstract = {Analytic second derivatives of electrostatic embedding (EE) quantum mechanics/molecular mechanics (QM/MM) energy are important for performing vibrational analysis and simulating vibrational spectra of quantum systems interacting with an environment represented as a classical electrostatic potential. The main bottleneck of EE-QM/MM second derivatives is the solution of coupled perturbed equations for each MM atom perturbation. Here, we exploit the Q-vector method [J. Chem. Phys., 2019, 151, 041102] to workaround this bottleneck. We derive the full analytic second derivative of the EE-QM/MM energy, which allows us to compute QM, MM, and QM-MM Hessian blocks in an efficient and easy to implement manner. To show the capabilities of our method, we compute the normal modes for the full Arabidopsis thaliana plant cryptochrome. We show that the flavin adenine dinucleotide vibrations (QM subsystem) strongly mix with protein modes. We compute approximate vibronic couplings for the lowest bright transition, from which we extract spectral densities and the homogeneous broadening of FAD absorption spectrum in protein using vibrationally resolved electronic spectrum simulations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{refId0c,

title = {Basis function expansions for galactic dynamics: Spherical versus cylindrical coordinates},

author = {Y } {Wang and E } {Athanassoula and S } {Mao},

url = {https://doi.org/10.1051/0004-6361/202038225},

doi = {10.1051/0004-6361/202038225},

year  = {2020},

date = {2020-01-01},

journal = {A&A},

volume = {639},

pages = {A38},

abstract = {Aims. The orbital structure of galaxies is strongly influenced by the accuracy of the force calculation during orbit integration. We explore the accuracy of force calculations for two expansion methods and determine which one is preferable for orbit integration.



Methods. We specifically compare two methods, one was introduced by Hernquist & Ostriker (HO), which uses a spherical coordinate system and was built specifically for the Hernquist model, and the other by Vasiliev & Athanassoula (CylSP) has a cylindrical coordinate system. Our comparisons include the Dehnen profile, its triaxial extension (of which the Hernquist profile is a special case) and a multicomponent system including a bar and disk density distributions for both analytical models and N-body realizations.



Results. For the generalized Dehnen density, the CylSP method is more accurate than the HO method for nearly all inner power-law indices and shapes at all radii. For N-body realizations of the Dehnen model, or snapshots of an N-body simulation, the CylSP method is more accurate than the HO method in the central region for the oblate, prolate, and triaxial Hernquist profiles if the particle number is more than 5 × 105. For snapshots of the Hernquist models with spherical shape, the HO method is preferred. For the Ferrers bar model, the force from the CylSP method is more accurate than the HO method. The CPU time required for the initialization of the HO method is significantly shorter than that for the CylSP method, while the HO method costs subsequently much more CPU time than the CylSP method if the input corresponds to particle positions. From surface of section analyses, we find that the HO method creates more chaotic orbits than the CylSP method in the bar model. This could be understood to be due to a spurious peak in the central region when the force is calculated with the HO expansion.



Conclusions. For an analytical model, the CylSP method with an inner cutoff radius of interpolation Rmin as calculated by the AGAMA software, is preferred due to its accuracy. For snapshots or N-body realizations not including a disk or a bar component, a detailed comparison between these two methods is needed if a density model other than the Dehnen model is used. For multicomponent systems, including a disk and a bar, the CylSP method is preferable.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{EYMEOUD2020167223,

title = {Magnetic behavior of transition metal solutes in α-iron: A classification},

author = {Paul Eyméoud and Philippe Maugis},

url = {http://www.sciencedirect.com/science/article/pii/S0304885320311902},

doi = {https://doi.org/10.1016/j.jmmm.2020.167223},

issn = {0304-8853},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Magnetism and Magnetic Materials},

volume = {513},

pages = {167223},

abstract = {For several transition metals M, we have computed atomic magnetic moments for the body-centered cubic substitutional solid solution Fe1-xMx, by two comparative first-principle approaches for atomic disorder: Korringa-Kohn-Rostoker Coherent Potential Approximation (KKR-CPA) and Density Functional Theory applied to Special Quasirandom Structures (SQS-DFT). Our results, compared with experimental and numerical literature, led to a classification of transition metal solutes in α-iron with respect to their magnetic behavior.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ISI:000493158900001,

title = {pH-Dependent Absorption Spectrum of Oxyluciferin Analogues in the  Presence of Adenosine Monophosphate},

author = {Nuno Manuel Almeida de Barbosa and Madjid Zemmouche and Pauline Gosset and Cristina Garcia-Iriepa and Vincent Ledentu and Isabelle Navizet and Pascal Didier and Nicolas Ferre},

doi = {10.1002/cptc.201900150, Early Access Date = OCT 2019},

issn = {2367-0932},

year  = {2019},

date = {2019-12-13},

journal = {CHEMPHOTOCHEM},

publisher = {WILEY-V C H VERLAG GMBH},

address = {POSTFACH 101161, 69451 WEINHEIM, GERMANY},

abstract = {The photophysical properties of oxyluciferin, the light emitter 

 responsible for firefly bioluminescence, are pH-dependent. One of the 

 potential proton acceptor/donor is adenosine monophosphate (AMP). We 

 have studied three oxyluciferin synthetic analogues with or without AMP, in water, in the pH=5 to 11 range, using both experimental steady-state 

 absorption spectroscopy or the recently developed computational protocol 

 that uses constant pH molecular dynamics and then hybrid QM/MM 

 calculations (CpHMD-then-QM/MM). The latter features a systematic 

 investigation of all the protonation microstates using molecular 

 dynamics simulations coupled to thousands hybrid QM/MM vertical 

 excitation energies. Our results demonstrate that AMP does not 

 significantly modify the visible light absorption of the analogues, 

 whatever the pH value. We also show that CpHMD-then-QM/MM is capable to 

 qualitatively reproduce the pH-dependent absorption spectrum of the 

 analogues, despite the employed low QM level of theory.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ISI:000490988300066,

title = {Genome editing retraces the evolution of toxin resistance in the monarch 

 butterfly},

author = {Marianthi Karageorgi and Simon C Groen and Fidan Sumbul and Julianne N Pelaez and Kirsten I Verster and Jessica M Aguilar and Amy P Hastings and Susan L Bernstein and Teruyuki Matsunaga and Michael Astourian and Geno Guerra and Felix Rico and Susanne Dobler and Anurag A Agrawal and Noah K Whiteman},

doi = {10.1038/s41586-019-1610-8},

issn = {0028-0836},

year  = {2019},

date = {2019-10-01},

journal = {NATURE},

volume = {574},

number = {7778},

pages = {409+},

publisher = {NATURE PUBLISHING GROUP},

address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},

abstract = {Identifying the genetic mechanisms of adaptation requires the 

 elucidation of links between the evolution of DNA sequence, phenotype, 

 and fitness(1). Convergent evolution can be used as a guide to identify 

 candidate mutations that underlie adaptive traits(2-4), and new genome 

 editing technology is facilitating functional validation of these 

 mutations in whole organisms(1,5). We combined these approaches to study 

 a classic case of convergence in insects from six orders, including the 

 monarch butterfly (Danaus plexippus), that have independently evolved to 

 colonize plants that produce cardiac glycoside toxins(6-11). Many of 

 these insects evolved parallel amino acid substitutions in the 

 alpha-subunit (ATP alpha) of the sodium pump (Na+/K+-ATPase)(7-11), the 

 physiological target of cardiac glycosides(12). Here we describe 

 mutational paths involving three repeatedly changing amino acid sites 

 (111, 119 and 122) in ATP alpha that are associated with cardiac 

 glycoside specialization(13,14). We then performed CRISPR-Cas9 base 

 editing on the native Atp alpha gene in Drosophila melanogaster flies 

 and retraced the mutational path taken across the monarch 

 lineage(11,15). We show in vivo, in vitro and in silico that the path 

 conferred resistance and target-site insensitivity to cardiac 

 glycosides(16), culminating in triple mutant `monarch flies' that were 

 as insensitive to cardiac glycosides as monarch butterflies. `Monarch 

 flies' retained small amounts of cardiac glycosides through 

 metamorphosis, a trait that has been optimized in monarch butterflies to 

 deter predators(17-19.) The order in which the substitutions evolved was 

 explained by amelioration of antagonistic pleiotropy through 

 epistasis(13,14,20-22). Our study illuminates how the monarch butterfly 

 evolved resistance to a class of plant toxins, eventually becoming 

 unpalatable, and changing the nature of species interactions within 

 ecological communities(2,6-11,15,17-19).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}