@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{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{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{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{TAYYAB2020103,
title = {Experimental and numerical Lattice-Boltzmann investigation of the Darrieus–Landau instability},
author = {Muhammad Tayyab and Basile Radisson and Christophe Almarcha and Bruno Denet and Pierre Boivin},
url = {http://www.sciencedirect.com/science/article/pii/S001021802030300X},
doi = {https://doi.org/10.1016/j.combustflame.2020.07.030},
issn = {0010-2180},
year = {2020},
date = {2020-01-01},
journal = {Combustion and Flame},
volume = {221},
pages = {103 - 109},
abstract = {We present an experimental and numerical investigation of the Darrieus–Landau instability in a quasi two-dimensional Hele-Shaw cell. Experiments and Lattice-Boltzmann numerical simulations are compared with Darrieus–Landau analytical theory, showing an excellent agreement for the exponential growth rate of the instability in the linear regime. The negative growth rate – second solution of the dispersion relation – was also measured numerically for the first time to the authors’ knowledge. Experiments and numerical simulations were then carried out beyond the cutoff wavelength, providing good agreement even in the unexplored regime where Darrieus–Landau is supplanted by diffusive stabilization. Lastly, the non-linear evolution involving the merging of crests on the experimental flame front is also successfully recovered using both the Michelson–Sivashinsky equation integration and the Lattice-Boltzmann simulation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{oujia:hal-02655795,
title = {Divergence and convergence of inertial particles in high Reynolds number turbulence},
author = {Thibault Oujia and Keigo Matsuda and Kai Schneider},
url = {https://hal.archives-ouvertes.fr/hal-02655795},
doi = {10.1017/jfm.2020.672},
year = {2020},
date = {2020-01-01},
journal = {Journal of Fluid Mechanics},
publisher = {Cambridge University Press (CUP)},
abstract = {Inertial particle data from three-dimensional direct numerical simulations of particle-laden homogeneous isotropic turbulence at high Reynolds number are analyzed using Voronoi tessellation of the particle positions, considering different Stokes numbers. A finite-time measure to quantify the divergence of the particle velocity by determining the volume change rate of the Voronoi cells is proposed. For inertial particles the probability distribution function (PDF) of the divergence deviates from that for fluid particles. Joint PDFs of the divergence and the Voronoi volume illustrate that the divergence is most prominent in cluster regions and less pronounced in void regions. For larger volumes the results show negative divergence values which represent cluster formation (i.e. particle convergence) and for small volumes the results show positive divergence values which represents cluster destruction/void formation (i.e. particle divergence). Moreover, when the Stokes number increases the divergence takes larger values, which gives some evidence why fine clusters are less observed for large Stokes numbers. Theoretical analyses further show that the divergence for random particles in random flow satisfies a PDF corresponding to the ratio of two independent variables following normal and gamma distributions in one dimension. Extending this model to three dimensions, the predicted PDF agrees reasonably well with Monte-Carlo simulations and DNS data of fluid particles. },
note = {23 pages, 9 figures},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{legal:hal-02978216,
title = {The instability of the vertically-stratified horizontal plane Poiseuille flow},
author = {P Le Gal and U Harlander and I Borcia and Stéphane Le Dizes and J Chen and B Favier},
url = {https://hal.archives-ouvertes.fr/hal-02978216},
year = {2020},
date = {2020-01-01},
journal = {Journal of Fluid Mechanics},
publisher = {Cambridge University Press (CUP)},
abstract = {We present here the first study on the stability of the plane Poiseuille flow when the fluid is stratified in density perpendicularly to the plane of the horizontal shear. Using laboratory experiments, linear stability analyses and direct numerical simulations, we describe the appearance of an instability that results from a resonance of internal gravity waves and Tollmien-Schlichting waves carried by the flow. This instability takes the form of long meanders confined in thin horizontal layers stacked along the vertical axis. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{TRUONG2020382,
title = {Influence of wing flexibility on the aerodynamic performance of a tethered flapping bumblebee},
author = {Hung Truong and Thomas Engels and Dmitry Kolomenskiy and Kai Schneider},
url = {http://www.sciencedirect.com/science/article/pii/S2095034920300684},
doi = {https://doi.org/10.1016/j.taml.2020.01.056},
issn = {2095-0349},
year = {2020},
date = {2020-01-01},
journal = {Theoretical and Applied Mechanics Letters},
volume = {10},
number = {6},
pages = {382 - 389},
abstract = {EDITOR'S RECOMMENDATION
The flight of insects has enlightened the flying dream of human beings for centuries. Wing flexibility is often used by insects to increase their flight efficiencies. However, the mechanism of the increased efficiencies still remains mysterious. Prof. Kai Schneider's group studies the aerodynamics of a tethered flapping bumblebee using a mass-spring fluid-structure interaction numerical solver. It indicates that a higher flight efficiency or a larger lift-to-power ratio can be achieved by flapping insects with optimal mechanical properties of the flexible wings. The novel understanding of insects’ body structure and flying behavior will benefit the design of micro-air vehicles (MAVs).
ABSTRACT
The sophisticated structures of flapping insect wings make it challenging to study the role of wing flexibility in insect flight. In this study, a mass-spring system is used to model wing structural dynamics as a thin, flexible membrane supported by a network of veins. The vein mechanical properties can be estimated based on their diameters and the Young's modulus of cuticle. In order to analyze the effect of wing flexibility, the Young's modulus is varied to make a comparison between two different wing models that we refer to as flexible and highly flexible. The wing models are coupled with a pseudo-spectral code solving the incompressible Navier–Stokes equations, allowing us to investigate the influence of wing deformation on the aerodynamic efficiency of a tethered flapping bumblebee. Compared to the bumblebee model with rigid wings, the one with flexible wings flies more efficiently, characterized by a larger lift-to-power ratio.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{huixrotllant:hal-03066310,
title = {Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of blue-light-induced infrared spectra of arabidopsis thaliana plant cryptochrome},
author = {Miquel Huix-Rotllant and Karno Schwinn and Nicolas Ferré},
url = {https://hal.archives-ouvertes.fr/hal-03066310},
doi = {10.1039/D0CP06070D},
year = {2020},
date = {2020-01-01},
journal = {Physical Chemistry Chemical Physics},
publisher = {Royal Society of Chemistry},
abstract = {Infrared (IR) spectroscopy of biological macromolecules is an undoubtedly valuable tool for analyzing chemical reactions. Currently, there is a lack of theoretical methods able to model successfully and efficiently simulate and interpret the origin of the spectral signatures. Here, we develop a new method for IR vibrational spectroscopy based on analytic second derivatives of electrostatic embedding QM/MM energy, the computation of electric dipole moments with respect to nuclear perturbations and the localization of normal modes. In addition to the spectrum, the method can provide the origin of each peak from clearly identified molecular motions. As proof of concept, we analyze the IR spectra of flavin adenine dinucleotide in water and in arabidopsis thaliana cryptochrome protein for four redox forms, and the difference IR spectrum before and after illumination with blue light. We show that the main peaks in the difference spectrum are due to N−H hydrogen out-of-plane motions and hydrogen bendings. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{kumar:hal-03079035,
title = {Turbulent transport driven by kinetic ballooning modes in the inner core of JET hybrid H-modes},
author = {Neeraj Kumar and Yann Camenen and Sadruddin Benkadda and Clarisse Bourdelle and Alberto Loarte and Alexei R Polevoi and Fabien Widmer},
url = {https://hal.archives-ouvertes.fr/hal-03079035},
doi = {10.1088/1741-4326/abd09c},
year = {2020},
date = {2020-01-01},
journal = {Nuclear Fusion},
publisher = {IOP Publishing},
abstract = {Turbulent transport in the inner core of the high-β JET hybrid discharge 75225 is investigated extensively through linear and non-linear gyrokinetic simulations using the gyro-kinetic code GKW in the local approximation limit. Compared to previous studies [J. Citrin et al. 2015 Plasma Phys. Control. Fusion 57 014032, J. Garcia et al. 2015 Nucl. Fusion 55 053007], the analysis has been extended towards the magnetic axis, ρ < 0.3, where the turbulence characteristics remain an open question. Understanding turbulent transport in this region is crucial to predict core profile peaking that in turn will impact the fusion reactions and the tungsten neoclassical transport, in present devices as well as in ITER. At ρ = 0.15, a linear stability analysis indicates that Kinetic Ballooning Modes (KBMs) dominate, with an extended mode structure in ballooning space due to the low magnetic shear. The sensitivity of KBM stability to main plasma parameters is investigated. In the non-linear regime, the turbulence induced by these KBMs drives a significant ion and electron heat flux. Standard quasi-linear models are compared to the non-linear results. The standard reduced quasi-linear models work well for the E × B fluxes, but fail to capture magnetic flutter contribution to the electron heat flux induced by the non-linear excitation of low k θ ρ i micro-tearing modes that are linearly stable. An extension of the quasi-linear models is proposed allowing better capturing the magnetic flutter flux. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}