@article{Alías-Rodríguez2023,

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

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

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

issn = {1520-5215},

year  = {2023},

date = {2023-12-14},

urldate = {2023-12-14},

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

volume = {127},

number = {49},

pages = {10382--10392},

publisher = {American Chemical Society (ACS)},

abstract = {The accurate description of solvent effects on X-ray absorption spectra (XAS) is fundamental for comparing the simulated spectra with experiments in solution. Currently, few protocols exist that can efficiently reproduce the effects of the solute/solvent interactions on XAS. Here, we develop an efficient and accurate theoretical protocol for simulating the solvent effects on XAS. The protocol combines electrostatic embedding QM/MM based on electrostatic potential fitted operators for describing the solute/solvent interactions and mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for simulating accurate XAS spectra. To demonstrate the capabilities of our protocol, we compute the X-ray absorption of neutral proline in the gas phase and ionic proline in water in all relevant K-edges, showing excellent agreement with experiments. We show that states represented by core to π* transitions are almost unaffected by the interaction with water, whereas the core to σ* transitions are more impacted by the fluctuation of proline structure and the electrostatic interaction with the solvent. Finally, we reconstruct the pH-dependent XAS of proline in solution, determining that the N K-edge can be used to distinguish its three protonation states.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jonckheere2023,

title = {Quartet currents in a biased three-terminal diffusive Josephson junction},

author = {T. Jonckheere and J. Rech and C. Padurariu and L. Raymond and T. Martin and D. Feinberg},

doi = {10.1103/physrevb.108.214517},

issn = {2469-9969},

year  = {2023},

date = {2023-12-12},

journal = {Phys. Rev. B},

volume = {108},

number = {21},

publisher = {American Physical Society (APS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wissocq2023,

title = {A hybrid lattice Boltzmann method for gaseous detonations},

author = {Gauthier Wissocq and Said Taileb and Song Zhao and Pierre Boivin},

doi = {10.1016/j.jcp.2023.112525},

issn = {0021-9991},

year  = {2023},

date = {2023-12-01},

urldate = {2023-12-01},

journal = {Journal of Computational Physics},

volume = {494},

publisher = {Elsevier BV},

abstract = {This article is dedicated to the construction of a robust and accurate numerical scheme based on the lattice Boltzmann method (LBM) for simulations of gaseous detonations. This objective is achieved through careful construction of a fully conservative hybrid lattice Boltzmann scheme tailored for multi-species reactive flows. The core concept is to retain LBM low dissipation properties for acoustic and vortical modes by using the collide and stream algorithm for the particle distribution function, while transporting entropic and species modes via a specifically designed finite-volume scheme. The proposed method is first evaluated on common academic cases, demonstrating its ability to accurately simulate multi-species compressible and reactive flows with discontinuities: the convection of inert species, a Sod shock tube with two ideal gases and a steady one-dimensional inviscid detonation wave. Subsequently, the potential of this novel approach is demonstrated in one- and two-dimensional inviscid unsteady gaseous detonations, highlighting its ability to accurately recover detonation structures and associated instabilities for high activation energies. To the authors' knowledge, this study is the first successful simulation of detonation cellular structures capitalizing on the LBM collide and stream algorithm.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cárdenas2023,

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

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

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

issn = {1520-5215},

year  = {2023},

date = {2023-11-09},

urldate = {2023-11-09},

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

volume = {127},

number = {44},

pages = {9365--9380},

publisher = {American Chemical Society (ACS)},

abstract = {Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LiManni2023,

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

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

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

issn = {1549-9626},

year  = {2023},

date = {2023-10-24},

urldate = {2023-10-24},

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

volume = {19},

number = {20},

pages = {6933--6991},

publisher = {American Chemical Society (ACS)},

abstract = {The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{He2023,

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

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

doi = {10.1017/jfm.2023.761},

issn = {1469-7645},

year  = {2023},

date = {2023-10-23},

journal = {J. Fluid Mech.},

volume = {974},

publisher = {Cambridge University Press (CUP)},

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

	      

		

		$E^{1/3}$

	      

	     and 

	      

		

		$E^{1/12}$

	      

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

	      

		

		$E^{1/6}$

	      

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

	      

		

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

	      

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

	      

		

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

	      

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mansour2023,

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

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

doi = {10.1039/d3cp03234e},

issn = {1463-9084},

year  = {2023},

date = {2023-10-18},

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

volume = {25},

number = {40},

pages = {27083--27093},

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

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sun2023,

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

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

doi = {10.1002/anie.202310436},

issn = {1521-3773},

year  = {2023},

date = {2023-10-16},

urldate = {2023-10-16},

journal = {Angew Chem Int Ed},

volume = {62},

number = {42},

publisher = {Wiley},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{deLangen2023,

title = {Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues},

author = {Pierre de Langen and Fayrouz Hammal and Elise Guéret and Jean-Christophe Mouren and Lionel Spinelli and Benoit Ballester},

doi = {10.1016/j.xgen.2023.100411},

issn = {2666-979X},

year  = {2023},

date = {2023-10-11},

urldate = {2023-10-11},

journal = {Cell Genomics},

volume = {3},

number = {10},

publisher = {Elsevier BV},

abstract = {Intergenic transcription in normal and cancerous tissues is pervasive but incompletely understood. To investigate this, we constructed an atlas of over 180,000 consensus RNA polymerase II (RNAPII)-bound intergenic regions from 900 RNAPII chromatin immunoprecipitation sequencing (ChIP-seq) experiments in normal and cancer samples. Through unsupervised analysis, we identified 51 RNAPII consensus clusters, many of which mapped to specific biotypes and revealed tissue-specific regulatory signatures. We developed a meta-clustering methodology to integrate our RNAPII atlas with active transcription across 28,797 RNA sequencing (RNA-seq) samples from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Encyclopedia of DNA Elements (ENCODE). This analysis revealed strong tissue- and disease-specific interconnections between RNAPII occupancy and transcriptional activity. We demonstrate that intergenic transcription at RNAPII-bound regions is a novel per-cancer and pan-cancer biomarker. This biomarker displays genomic and clinically relevant characteristics, distinguishing cancer subtypes and linking to overall survival. Our results demonstrate the effectiveness of coherent data integration to uncover intergenic transcriptional activity in normal and cancer tissues. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Faux2023,

title = {Neanderthal introgression in SCN9A impacts mechanical pain sensitivity},

author = {Pierre Faux and Li Ding and Luis Miguel Ramirez-Aristeguieta and J. Camilo Chacón-Duque and Maddalena Comini and Javier Mendoza-Revilla and Macarena Fuentes-Guajardo and Claudia Jaramillo and William Arias and Malena Hurtado and Valeria Villegas and Vanessa Granja and Rodrigo Barquera and Paola Everardo-Martínez and Mirsha Quinto-Sánchez and Jorge Gómez-Valdés and Hugo Villamil-Ramírez and Caio C. Silva de Cerqueira and Tábita Hünemeier and Virginia Ramallo and Rolando Gonzalez-José and Lavinia Schüler-Faccini and Maria-Cátira Bortolini and Victor Acuña-Alonzo and Samuel Canizales-Quinteros and Giovanni Poletti and Carla Gallo and Francisco Rothhammer and Winston Rojas and Annina B. Schmid and Kaustubh Adhikari and David L. Bennett and Andrés Ruiz-Linares},

doi = {10.1038/s42003-023-05286-z},

issn = {2399-3642},

year  = {2023},

date = {2023-10-10},

urldate = {2023-10-10},

journal = {Commun Biol},

volume = {6},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tessier2023,

title = {Quantitative MRI of Gd-DOTA Accumulation in the Mouse Brain After Intraperitoneal Administration: Validation by Mass Spectrometry},

author = {Anthony Tessier and Anthony J. Ruze and Isabelle Varlet and Estelle M.H. Laïb and Emilien Royer and Monique Bernard and Angèle Viola and Teodora‐Adriana Perles‐Barbacaru},

doi = {10.1002/jmri.29034},

issn = {1522-2586},

year  = {2023},

date = {2023-10-09},

urldate = {2023-10-09},

journal = {Magnetic Resonance Imaging},

volume = {60},

number = {1},

pages = {316--324},

publisher = {Wiley},

abstract = {In mice, intraperitoneal (ip) contrast agent (CA) administration is convenient for mapping microvascular parameters over a long-time window. However, continuous quantitative MRI of CA accumulation in brain over hours is still missing.

Purpose



To validate a quantitative time-resolved MRI technique for mapping the CA kinetics in brain upon ip administration.

Study Type



Prospective, animal model.

Specimen



25 C57Bl/6JRj mice underwent MRI.

Field Strength/Sequence



7-T, gradient echo sequence.

Assessment



Gd-DOTA concentration was monitored by MRI (25 s/repetition) over 135 minutes with (N = 15) and without (N = 10) ip mannitol challenge (5 g/kg). After the final repetition, the brains were sampled to quantify gadolinium by mass spectrometry (MS). Upon manual brain segmentation, the average gadolinium concentration was compared with the MS quantification in transcardially perfused (N = 20) and unperfused (N = 5) mice. Precontrast T1-maps were acquired in 8 of 25 mice.

Statistical Tests



One-tailed Spearman and Pearson correlation between gadolinium quantification by MRI and by MS, D'Agostino-Pearson test for normal distribution, Bland–Altman analysis to evaluate the agreement between MRI and MS. Significance was set at P-value <0.05.

Results



MRI showed that ip administered CA reached the blood compartment (>5 mM) within 10 minutes and accumulated continuously for 2 hours in cerebrospinal fluid (>1 mM) and in brain tissue. The MRI-derived concentration maps showed interindividual differences in CA accumulation (from 0.47 to 0.81 mM at 2 hours) with a consistent distribution resembling the pathways of the glymphatic system. The average in-vivo brain concentration 2 hours post-CA administration correlated significantly (r = 0.8206) with the brain gadolinium quantification by MS for N = 21 paired observations available.

Data Conclusion



The presented experimental and imaging protocol may be convenient for monitoring the spatiotemporal pattern of CA uptake and clearance in the mouse brain over 2 hours. The quantification of the CA from the MRI signal in brain is corroborated by MS.

Evidence Level



N/A

Technical Efficacy



Stage 1

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dalton2023,

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

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

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

issn = {1948-7185},

year  = {2023},

date = {2023-10-05},

urldate = {2023-10-05},

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

volume = {14},

number = {39},

pages = {8771--8779},

publisher = {American Chemical Society (ACS)},

abstract = {Two model biomimetic systems, ethyl sinapate (ES) and its symmetrical analogue, diethyl 2-(4-hydroxy-3,5-dimethoxybenzylidene)malonate (or diethyl sinapate, DES), are stripped to their core fundamentals through gas-phase spectroscopy to understand the underlying photophysics of photothermal materials. Following photoexcitation to the optically bright S1(ππ*) state, DES is found to repopulate the electronic ground state over 3 orders of magnitude quicker than its nonsymmetrical counterpart, ES. Our XMS-CASPT2 calculations shed light on the experimental results, revealing crucial differences in the potential energy surfaces and conical intersection topography between ES and DES. From this work, a peaked conical intersection, seen for DES, shows vital importance for the nonradiative ground-state recovery of photothermal materials. This fundamental comparative study highlights the potential impact that symmetrical substitution can have on the photodynamics of sinapate esters, providing a blueprint for future advancement in photothermal technology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Crépieux2023,

title = {Superconductivity in monolayer and few-layer graphene. II. Topological edge states and Chern numbers},

author = {Adeline Crépieux and Emile Pangburn and Louis Haurie and Oladunjoye A. Awoga and Annica M. Black-Schaffer and Nicholas Sedlmayr and Catherine Pépin and Cristina Bena},

doi = {10.1103/physrevb.108.134515},

issn = {2469-9969},

year  = {2023},

date = {2023-10-01},

journal = {Phys. Rev. B},

volume = {108},

number = {13},

publisher = {American Physical Society (APS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Alías-Rodríguez2023b,

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

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

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

issn = {1948-7185},

year  = {2023},

date = {2023-09-28},

urldate = {2023-09-28},

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

volume = {14},

number = {38},

pages = {8571--8576},

publisher = {American Chemical Society (ACS)},

abstract = {Photoexcitation of [FeII(2,2′-bipyridine)3]2+ induces a subpicosecond spin crossover transformation from a low-spin singlet to a high-spin quintet state. The mechanism involves metal-centered (MC) and metal–ligand charge transfer (MLCT) triplet intermediates, but their individual contributions to this efficient intersystem crossing have been object of debate. Employing quantum wavepacket dynamics, we show that MC triplets are catalyzing the transfer to the high-spin state. This photochemical pathway is made possible thanks to bipyridine stretching vibrations, facilitating the conversion between the MLCT bands to such MC triplets. We show that the lifetime of the MLCT states can be increased to tens of picoseconds by breaking the conjugation between pyridine units, which increases the energetic gap between MLCT and MC states. This opens the route for the design of new chelating ligands inducing long-lived MLCT states in iron complexes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001014762300001,

title = {Solver comparison for Poisson-like equations on tokamak geometries},

author = {Emily Bourne and Philippe Leleux and Katharina Kormann and Carola Kruse and Virginie Grandgirard and Yaman Guclu and Martin J. Kuhn and Ulrich Rude and Eric Sonnendrucker and Edoardo Zoni},

doi = {10.1016/j.jcp.2023.112249},

issn = {0021-9991},

year  = {2023},

date = {2023-09-01},

journal = {JOURNAL OF COMPUTATIONAL PHYSICS},

volume = {488},

publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},

address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},

abstract = {The solution of Poisson-like equations defined on a complex geometry is 

 required for gyrokinetic simulations, which are important for the 

 modelling of plasma turbulence in nuclear fusion devices such as the 

 ITER tokamak. In this paper, we compare three existing solvers finely 

 tuned to solve this problem, in terms of the accuracy of the solution, 

 and their computational efficiency. We also consider practical 

 implementation aspects, including the parallel efficiency of the code, 

 potentially enabling an integration of the solvers in a state-of-the-art 

 first-principle gyrokinetic simulation framework. The first, the Spline 

 FEM solver, uses C1 polar splines to construct a finite elements method 

 which solves the equation on curvilinear coordinates. The resulting 

 linear system is solved using a conjugate gradient method. The second, 

 the GMGPolar solver, uses a symmetric finite difference method to 

 discretise the differential equation. The resulting linear system is 

 solved using a tailored geometric multigrid scheme, with a combination 

 of zebra circle and radial line smoothers, together with an implicit 

 extrapolation scheme. The third, the Embedded Boundary solver, uses a 

 finite volumes method on Cartesian coordinates with an embedded boundary 

 scheme. The resulting linear system is solved using a multigrid scheme. 

 The Spline FEM solver is shown to be the most accurate. The GMGPolar 

 solver is shown to use the least memory. The Embedded Boundary solver is 

 shown to be the fastest in most cases. All three solvers are shown to be 

 capable of solving the equation on a realistic non-analytical geometry. 

 The Embedded Boundary solver is additionally used to attempt to solve an 

 X-point geometry.(C) 2023 Elsevier Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001013577700001,

title = {Non-uniform splines for semi-Lagrangian kinetic simulations of the 

 plasma sheath},

author = {Emily Bourne and Yann Munschy and Virginie Grandgirard and Michel Mehrenberger and Philippe Ghendrih},

doi = {10.1016/j.jcp.2023.112229},

issn = {0021-9991},

year  = {2023},

date = {2023-09-01},

journal = {JOURNAL OF COMPUTATIONAL PHYSICS},

volume = {488},

abstract = {Numerical methods based on non-uniform splines of varying degrees are 

 used to run kinetic semi-Lagrangian simulations of the plasma sheath. 

 The sheath describes a region of plasma in contact with a wall, acting 

 as a heat, momentum, and particle bath. The latter regulates the current 

 loss and consequently the electric field. At micro scale it then 

 influences the development of plasma turbulence and at a larger scale 

 plasma rotation. However this region is particularly difficult to 

 simulate, due to its kinetic nature and the presence of steep gradients 

 requiring fine numerical resolution. In this work, a new well 

 -conditioned method for determining the coefficients for Schoenberg's 

 ``best'' quadrature is presented, providing improved precision 

 compared to a naive approach based on b-spline derivatives (4 extra 

 significant figures of precision are obtained for coefficients of the 

 fifth order scheme). The construction of a simulation grid from Greville 

 abcissae of judiciously chosen non-uniform knots is shown to reduce the 

 memory requirements by 89% for the simulation presented. Cubic splines 

 are found to provide a good compromise between fast convergence and 

 controlled oscillations preserving positivity. Despite the reduction in 

 performance associated with using non-uniform spline schemes, effective 

 parallelisation through the use of GPUs leads to non-uniform simulations 

 running 5.5 times faster than uniform simulations providing equivalent 

 results. & COPY; 2023 Elsevier Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kriaa2023,

title = {Two-way coupling Eulerian numerical simulations of particle clouds settling in a quiescent fluid},

author = {Quentin Kriaa and Benjamin Favier and Michael Le Bars},

doi = {10.1103/physrevfluids.8.074302},

issn = {2469-990X},

year  = {2023},

date = {2023-07-18},

journal = {Phys. Rev. Fluids},

volume = {8},

number = {7},

publisher = {American Physical Society (APS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Millán-Merino2023,

title = {A new method for systematic 1-step chemistry reduction applied to hydrocarbon combustion},

author = {Alejandro Millán-Merino and Said Taileb and Pierre Boivin},

doi = {10.1016/j.proci.2022.08.052},

issn = {1540-7489},

year  = {2023},

date = {2023-06-07},

urldate = {2023-06-07},

journal = {Proceedings of the Combustion Institute},

volume = {39},

number = {1},

pages = {745--753},

publisher = {Elsevier BV},

abstract = {We propose a new single-step mechanism for the combustion of arbitrary hydrocarbons and alcohols. Unlike most single-step models, no tabulation is required, as the method builds upon a new analytical description of the thermochemical equilibrium of fuel-oxidizer mixtures including dihydrogen and carbon monoxide – two species usually discarded in one-step descriptions – yielding correct adiabatic temperature. The single-step chemistry includes varying stoichiometric coefficients, ensuring a convergence towards thermochemical equilibrium regardless of the local state. The reaction rate is then carefully adjusted to reproduce accurately premixed flames. To tackle ignition simultaneously, an additional passive scalar advection-diffusion-reaction equation is introduced, with a rate fitted on ignition delays. The scalar then serves as an efficiency to modify the single-step reaction rate in autoignition configurations. The obtained scheme is then validated for a wide range of equivalence ratios on homogeneous reactors, premixed flames, a triple flame, and a counterflow diffusion flame. The new analytical thermochemical equilibrium formulation may also serve in speeding up infinitely fast chemistry calculations.

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001000513500001,

title = {Imaging of the internal structure of an asteroid analogue from 

 quasi-monostatic microwave measurement data II. The time domain approach},

author = {Liisa-Ida Sorsa and Yusuf Oluwatoki Yusuf and Astrid Dufaure and Jean-Michel Geffrin and Christelle Eyraud and Sampsa Pursiainen},

doi = {10.1051/0004-6361/202244778},

issn = {0004-6361},

year  = {2023},

date = {2023-06-01},

journal = {ASTRONOMY & ASTROPHYSICS},

volume = {674},

abstract = {Context. The internal structures of small solar system bodies (SSSBs) 

 are still poorly understood. In this paper, we find an experimental 

 tomographic reconstruction of coarse high-contrast details inside a 

 complex-structured target object using multipoint full-wave radar 

 data.Aims. Our aim is to advance the development of inversion techniques 

 to be used in potential planetary scientific radar investigations 

 targeting SSSBs, which have complex shapes and whose internal structure 

 is largely unknown. Finding out the structure is an important scientific 

 objective of Solar System research in order to understand its history 

 and evolution.Methods. This is the second part (Paper II) of a joint 

 study considering the methods to analyse and invert quasi-monostatic 

 microwave measurement data of an asteroid analogue. We focused on 

 incorporating advanced, full-wave, forward simulation in time domain 

 with experimental data obtained from multiple measurement points. In 

 particular, this study investigates multiple scattering and multipath 

 effect suppression (MES) to reduce artefacts in the reconstructions. MES 

 is necessary since the high-contrast and complex-shaped target and, 

 especially, its back wall in high curvature regions cause intense 

 reflections that deteriorate the reconstruction quality if not treated 

 correctly. We considered the following two approaches to obtain MES: (i) 

 geometrical optics-based pathlength thresholding and (ii) a peak 

 detection method to investigate whether a data-driven approach could be 

 used. At the inversion stage, we investigated marginalisation of random 

 effects due to modelling by splitting a larger point set into several 

 sparse sets of measurements.Results. Based on the results, MES is 

 crucial to localise a void inside the complex analogue target. A 

 reconstruction can be found when the maximum signal propagation time 

 approximately matches that of the first back-wall echo for each 

 measurement point. The marginalisation approach allows us to find a 

 reconstruction that is comparable in quality to the case of full data, 

 while reducing the computation effort per subsystem, which is 

 advantageous when inverting a large data set.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001000513500005,

title = {Imaging of the internal structure of an asteroid analogue from 

 quasi-monostatic microwave measurement data I. The frequency domain 

 approach},

author = {A. Dufaure and C. Eyraud and L. - I Sorsa and Y. O. Yusuf and S. Pursiainen and J. -M Geffrin},

doi = {10.1051/0004-6361/202244777},

issn = {0004-6361},

year  = {2023},

date = {2023-06-01},

journal = {ASTRONOMY & ASTROPHYSICS},

volume = {674},

abstract = {Context. The internal structure of small Solar System bodies (SSSBs) is 

 still poorly understood, although it can provide important information 

 about the formation process of asteroids and comets. Space radars can 

 provide direct observations of this structure.Aims. In this study, we 

 investigate the possibility to infer the internal structure with a 

 simple and fast inversion procedure applied to radar measurements. We 

 consider a quasi-monostatic configuration with multiple measurements 

 over a wide frequency band, which is the most common configuration for 

 space radars. This is the first part (Paper I) of a joint study 

 considering methods to analyse and invert quasi-monostatic microwave 

 measurements of an asteroid analogue. This paper focuses on the 

 frequency domain, while a separate paper focuses on time-domain 

 methods.Methods. We carried out an experiment in the laboratory 

 equivalent to the probing of an asteroid using the microwave analogy 

 (multiplying the wavelength and the target dimension by the same 

 factor). Two analogues based on the shape of the asteroid 25143 Itokawa 

 were constructed with different interiors. The electromagnetic 

 interaction with these analogues was measured in an anechoic chamber 

 using a multi-frequency radar and a quasi-monostatic configuration. The 

 electric field was measured on 2372 angular positions (corresponding to 

 a sampling offering complete information). We then inverted these data 

 with two classical imaging procedures, allowing us to reach the 

 structural information of the analogues interior. We also investigated 

 reducing the number of radar measurements used in the imaging 

 procedures, that is both the number of transmitter-receiver pairs and 

 the number of frequencies.Results. The results show that the 3D map of 

 the analogues can be reconstructed without the need for a reference 

 target. Internal structural differences are distinguishable between the 

 analogues. This imaging can be achieved even with a reduced number of 

 measurements. With only 35 well-selected frequencies over 321 and 1257 

 transmitter-receiver pairs, the reconstructions are similar to those 

 obtained with the entire frequency band.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000987247600001,

title = {Immersed boundary based near-wall modeling for large eddy simulation of 

 turbulent wall-bounded flow},

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

doi = {10.1016/j.compfluid.2023.105893},

issn = {0045-7930},

year  = {2023},

date = {2023-06-01},

journal = {COMPUTERS & FLUIDS},

volume = {259},

abstract = {This paper describes the coupling of the immersed boundary method and 

 the near-wall modeling of large eddy simulation for high Reynolds number 

 turbulent flows over complex geometries on Cartesian grids. To overcome 

 the spurious oscillation problem arising from the imposition of boundary 

 conditions on the stair-case off-wall boundaries, several key 

 ingredients have been employed, such as interpolating the friction 

 velocity instead of the flow velocity from near-wall fluid interior 

 points, evaluating the gradients by the weighted least square method and 

 correcting the wall-normal gradient of the tangential velocity with the 

 law of the wall at the off-wall boundaries. Furthermore, a hybrid 

 RANS-LES approach has been applied to the near-wall eddy viscosity, 

 either through an empirical blending function or the Reynolds stress 

 balance constraint. We systematically discuss the effects of the hybrid 

 eddy viscosity in a turbulent channel flow and a high lift three 

 -element airfoil. Enforcing the Reynolds stress balance constraint turns 

 out to be very robust in the considered cases. For the high lift 

 three-element airfoil flow, the overall wall pressure and skin friction 

 are predicted reasonably well and smoothly. The flow details are in a 

 good agreement with the experimental data as well.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000993853100001,

title = {Lattice-Boltzmann modeling of the quiet and unstable PRECCINSTA burner 

 modes},

author = {Song Zhao and Karthik Bhairapurada and Muhammad Tayyab and Renaud Mercier and Pierre Boivin},

doi = {10.1016/j.compfluid.2023.105898},

issn = {0045-7930},

year  = {2023},

date = {2023-06-01},

journal = {COMPUTERS & FLUIDS},

volume = {260},

abstract = {Recent studies have shown that Lattice-Boltzmann methods are indeed very 

 promising in the field of reactive flows. More work is required, 

 however, to demonstrate its ability to tackle complex reacting cases, as 

 no study to the authors' knowledge - involves simultaneously high 

 Reynolds flows (for which the collision kernel needs specific care), 

 complex geometries (for which models are required at the wall 

 boundaries), and non-uniform grids (where non-conform meshes need to be 

 addressed). 

 The present study intends to fill that gap, by investigating the 

 well-known PRECCINSTA burner, including (i) characteristic boundary 

 conditions, (ii) classical turbulent combustion modeling, (iii) 

 multi-level grid refinements. Combining these elements, numerical 

 simulations of the PRECCINSTA burner are carried out, both for the quiet (phi = 0.83) and unstable regimes (phi = 0.7). In both regimes, results 

 are consistent with those obtained with classical (Navier-Stokes) 

 solvers, but at a much lower cost. In particular, it is the first time 

 that successful prediction of thermoacoustic instabilities in a complex 

 burner is shown in the framework of Lattice-Boltzmann methods.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Silvetti2023,

title = {Pressure dependence of electronic, vibrational and optical properties of wurtzite-boron nitride},

author = {Martino Silvetti and Claudio Attaccalite and Elena Cannuccia},

doi = {10.1103/physrevmaterials.7.055201},

issn = {2475-9953},

year  = {2023},

date = {2023-05-30},

journal = {Phys. Rev. Materials},

volume = {7},

number = {5},

publisher = {American Physical Society (APS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Li2023,

title = {Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape},

author = {Qing Li and Jieyi Chen and Pierre Faux and Miguel Eduardo Delgado and Betty Bonfante and Macarena Fuentes-Guajardo and Javier Mendoza-Revilla and J. Camilo Chacón-Duque and Malena Hurtado and Valeria Villegas and Vanessa Granja and Claudia Jaramillo and William Arias and Rodrigo Barquera and Paola Everardo-Martínez and Mirsha Sánchez-Quinto and Jorge Gómez-Valdés and Hugo Villamil-Ramírez and Caio C. Silva de Cerqueira and Tábita Hünemeier and Virginia Ramallo and Sijie Wu and Siyuan Du and Andrea Giardina and Soumya Subhra Paria and Mahfuzur Rahman Khokan and Rolando Gonzalez-José and Lavinia Schüler-Faccini and Maria-Cátira Bortolini and Victor Acuña-Alonzo and Samuel Canizales-Quinteros and Carla Gallo and Giovanni Poletti and Winston Rojas and Francisco Rothhammer and Nicolas Navarro and Sijia Wang and Kaustubh Adhikari and Andrés Ruiz-Linares},

doi = {10.1038/s42003-023-04838-7},

issn = {2399-3642},

year  = {2023},

date = {2023-05-08},

urldate = {2023-05-08},

journal = {Commun Biol},

volume = {6},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10<jats:sup>−8</jats:sup>) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000992563300001,

title = {Automatic landmarking identifies new loci associated with face 

 morphology and implicates Neanderthal introgression in human nasal shape},

author = {Qing Li and Jieyi Chen and Pierre Faux and Miguel Eduardo Delgado and Betty Bonfante and Macarena Fuentes-Guajardo and Javier Mendoza-Revilla and J. Camilo Chacon-Duque and Malena Hurtado and Valeria Villegas and Vanessa Granja and Claudia Jaramillo and William Arias and Rodrigo Barquera and Paola Everardo-Martinez and Mirsha Sanchez-Quinto and Jorge Gomez-Valdes and Hugo Villamil-Ramirez and Caio C. Silva de Cerqueira and Tabita Huenemeier and Virginia Ramallo and Sijie Wu and Siyuan Du and Andrea Giardina and Soumya Subhra Paria and Mahfuzur Rahman Khokan and Rolando Gonzalez-Jose and Lavinia Schueler-Faccini and Maria-Catira Bortolini and Victor Acuna-Alonzo and Samuel Canizales-Quinteros and Carla Gallo and Giovanni Poletti and Winston Rojas and Francisco Rothhammer and Nicolas Navarro and Sijia Wang and Kaustubh Adhikari and Andres Ruiz-Linares},

doi = {10.1038/s42003-023-04838-7},

year  = {2023},

date = {2023-05-01},

journal = {COMMUNICATIONS BIOLOGY},

volume = {6},

number = {1},

abstract = {A genome-wide association study and fully automatic landmarking approach 

 on frontal 2D face photographs of >6000 Latin Americans identifies novel 

 genomic regions influencing facial features and implicates Neanderthal 

 introgression in nasal shape. 

 We report a genome-wide association study of facial features in >6000 

 Latin Americans based on automatic landmarking of 2D portraits and 

 testing for association with inter-landmark distances. We detected 

 significant associations (P-value <5 x 10(-8)) at 42 genome regions, 

 nine of which have been previously reported. In follow-up analyses, 26 

 of the 33 novel regions replicate in East Asians, Europeans, or 

 Africans, and one mouse homologous region influences craniofacial 

 morphology in mice. The novel region in 1q32.3 shows introgression from 

 Neanderthals and we find that the introgressed tract increases nasal 

 height (consistent with the differentiation between Neanderthals and 

 modern humans). Novel regions include candidate genes and genome 

 regulatory elements previously implicated in craniofacial development, 

 and show preferential transcription in cranial neural crest cells. The 

 automated approach used here should simplify the collection of large 

 study samples from across the world, facilitating a cosmopolitan 

 characterization of the genetics of facial features.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000992568900005,

title = {Anyonic Statistics Revealed by the Hong-Ou-Mandel Dip for Fractional 

 Excitations},

author = {T. Jonckheere and J. Rech and B. Gremaud and T. Martin},

doi = {10.1103/PhysRevLett.130.186203},

issn = {0031-9007},

year  = {2023},

date = {2023-05-01},

journal = {PHYSICAL REVIEW LETTERS},

volume = {130},

number = {18},

abstract = {The fractional quantum Hall effect (FQHE) is known to host anyons, 

 quasiparticles whose statistics is intermediate between bosonic and 

 fermionic. We show here that Hong-Ou-Mandel (HOM) interferences between 

 excitations created by narrow voltage pulses on the edge states of a 

 FQHE system at low temperature show a direct signature of anyonic 

 statistics. The width of the HOM dip is universally fixed by the thermal 

 time scale, independently of the intrinsic width of the excited 

 fractional wave packets. This universal width can be related to the 

 anyonic braiding of the incoming excitations with thermal fluctuations 

 created at the quantum point contact. We show that this effect could be 

 realistically observed with periodic trains of narrow voltage pulses 

 using current experimental techniques.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000955149200001,

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

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

doi = {10.1039/d2sc06990c},

issn = {2041-6520},

year  = {2023},

date = {2023-04-01},

journal = {CHEMICAL SCIENCE},

volume = {14},

number = {15},

pages = {4012-4026},

abstract = {Electronic states with partial or complete doubly excited character play 

 a crucial role in many areas, such as singlet fission and non-linear 

 optical spectroscopy. Although doubly excited states have been studied 

 in polyenes and related systems for many years, the assignment as singly 

 vs. doubly excited, even in the simplest case of butadiene, has sparked 

 controversies. So far, no well-defined framework for classifying doubly 

 excited states has been developed, and even more, there is not even a 

 well-accepted definition of doubly excited character as such. Here, we 

 present a solution: a physically motivated definition of doubly excited 

 character based on operator expectation values and density matrices, 

 which works independently of the underlying orbital representation, 

 avoiding ambiguities that have plagued earlier studies. Furthermore, we 

 propose a classification scheme to differentiate three cases: (i) two 

 single excitations occurring within two independent pairs of orbitals 

 leaving four open shells (D-OS), (ii) the promotion of both electrons to 

 the same orbital, producing a closed-shell determinant (D-CS), and (iii) 

 a mixture of singly and doubly excited configurations not aligning with 

 either one of the previous cases (D-mix). We highlight their differences 

 in underlying energy terms and explain their signatures in practical 

 computations. The three cases are illustrated through various high-level 

 computational methods using dimers for D-OS, polyenes for D-mix, and 

 cyclobutane and tetrazine for D-CS. The conversion between D-OS and D-CS 

 is investigated using a well-known photochemical reaction, the 

 photodimerization of ethylene. This work provides a deeper understanding 

 of doubly excited states and may guide more rigorous discussions toward 

 improving their computational description while also giving insight into 

 their fundamental photophysics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000950499100004,

title = {Novel mouse models based on intersectional genetics to identify and 

 characterize plasmacytoid dendritic cells},

author = {Michael Valente and Nils Collinet and Thien-Phong Vu Manh and Dimitri Popoff and Khalissa Rahmani and Karima Naciri and Gilles Bessou and Rejane Rua and Laurine Gil and Cyrille Mionnet and Pierre Milpied and Elena Tomasello and Marc Dalod},

doi = {10.1038/s41590-023-01454-9},

issn = {1529-2908},

year  = {2023},

date = {2023-04-01},

journal = {NATURE IMMUNOLOGY},

volume = {24},

number = {4},

pages = {714+},

publisher = {NATURE PORTFOLIO},

address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},

abstract = {Plasmacytoid dendritic cells (pDCs) are the main source of type I 

 interferon (IFN-I) during viral infections. Their other functions are 

 debated, due to a lack of tools to identify and target them in vivo 

 without affecting pDC-like cells and transitional DCs (tDCs), which 

 harbor overlapping phenotypes and transcriptomes but a higher efficacy 

 for T cell activation. In the present report, we present a reporter 

 mouse, pDC-Tom, designed through intersectional genetics based on unique 

 Siglech and Pacsin1 coexpression in pDCs. The pDC-Tom mice specifically 

 tagged pDCs and, on breeding with Zbtb46(GFP) mice, enabled 

 transcriptomic profiling of all splenic DC types, unraveling diverging 

 activation of pDC-like cells versus tDCs during a viral infection. The 

 pDC-Tom mice also revealed initially similar but later divergent 

 microanatomical relocation of splenic IFN+ versus IFN- pDCs during 

 infection. The mouse models and specific gene modules we report here 

 will be useful to delineate the physiological functions of pDCs versus 

 other DC types. 

 Dalod and colleagues utilize a combinatorial genetic reporter strategy 

 to uniquely mark plasmacytoid dendritic cells (pDCs) in mice. They 

 utilize these mice to identify bona fide pDCs and functionally 

 characterize before and during viral infection, in comparison to several 

 other DC types.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000992461300003,

title = {Suppression of Wall Modes in Rapidly Rotating Rayleigh-Be ` nard 

 Convection by Narrow Horizontal Fins},

author = {Louise Terrien and Benjamin Favier and Edgar Knobloch},

doi = {10.1103/PhysRevLett.130.174002},

issn = {0031-9007},

year  = {2023},

date = {2023-04-01},

journal = {PHYSICAL REVIEW LETTERS},

volume = {130},

number = {17},

publisher = {AMER PHYSICAL SOC},

address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},

abstract = {The heat transport by rapidly rotating Rayleigh-Benard convection is of 

 fundamental importance to many geophysical flows. Laboratory 

 measurements are impeded by robust wall modes that develop along 

 vertical walls, significantly perturbing the heat flux. We show that 

 narrow horizontal fins along the vertical walls efficiently suppress 

 wall modes ensuring that their contribution to the global heat flux is 

 negligible compared with bulk convection in the geostrophic regime, 

 thereby paving the way for new experimental studies of geophysically 

 relevant regimes of rotating convection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000956387200002,

title = {Deep reinforcement learning for the olfactory search POMDP: a 

 quantitative benchmark},

author = {Aurore Loisy and Robin A. A. Heinonen},

doi = {10.1140/epje/s10189-023-00277-8},

issn = {1292-8941},

year  = {2023},

date = {2023-03-01},

journal = {EUROPEAN PHYSICAL JOURNAL E},

volume = {46},

number = {3},

abstract = {The olfactory search POMDP (partially observable Markov decision 

 process) is a sequential decision-making problem designed to mimic the 

 task faced by insects searching for a source of odor in turbulence, and 

 its solutions have applications to sniffer robots. As exact solutions 

 are out of reach, the challenge consists in finding the best possible 

 approximate solutions while keeping the computational cost reasonable. 

 We provide a quantitative benchmarking of a solver based on deep 

 reinforcement learning against traditional POMDP approximate solvers. We 

 show that deep reinforcement learning is a competitive alternative to 

 standard methods, in particular to generate lightweight policies 

 suitable for robots.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000932523900003,

title = {Swirling of vesicles: Shapes and dynamics in Poiseuille flow as a model 

 of RBC microcirculation},

author = {Jinming Lyu and Paul G. Chen and Alexander Farutin and Marc Jaeger and Chaouqi Misbah and Marc Leonetti},

doi = {10.1103/PhysRevFluids.8.L021602},

issn = {2469-990X},

year  = {2023},

date = {2023-02-01},

journal = {PHYSICAL REVIEW FLUIDS},

volume = {8},

number = {2},

abstract = {We report on a systematic numerical exploration of the vesicle dynamics 

 in a channel, which is a model of red blood cells in microcirculation. 

 We find a spontaneous transition, called swirling, from straight motion 

 with axisymmetric shape to a motion along a helix with a stationary 

 deformed shape that rolls on itself and spins around the flow direction. 

 We also report on a planar oscillatory motion of the mass center, called 

 three-dimensional snaking, for which the shape deforms periodically. 

 Both emerge from supercritical pitch-fork bifurcation with the same 

 threshold. The universality of these oscillatory dynamics emerges from 

 Hopf bifurcations with two order parameters. These two oscillatory 

 dy-namics are put in the context of vesicle shape and dynamics in the 

 parameter space of reduced volume v, capillary number, and confinement. Phase diagrams are established for v = 0.95},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:000944690700001,

title = {WS22 database, Wigner Sampling and geometry interpolation for 

 configurationally diverse molecular datasets},

author = {Max Pinheiro Jr and Shuang Zhang and Pavlo O. O. Dral and Mario Barbatti},

doi = {10.1038/s41597-023-01998-3},

year  = {2023},

date = {2023-02-01},

journal = {SCIENTIFIC DATA},

volume = {10},

number = {1},

abstract = {Multidimensional surfaces of quantum chemical properties, such as 

 potential energies and dipole moments, are common targets for machine 

 learning, requiring the development of robust and diverse databases 

 extensively exploring molecular configurational spaces. Here we composed 

 the WS22 database covering several quantum mechanical (QM) properties 

 (including potential energies, forces, dipole moments, polarizabilities, 

 HOMO, and LUMO energies) for ten flexible organic molecules of 

 increasing complexity and with up to 22 atoms. This database consists of 

 1.18 million equilibrium and non-equilibrium geometries carefully 

 sampled from Wigner distributions centered at different equilibrium 

 conformations (either at the ground or excited electronic states) and 

 further augmented with interpolated structures. The diversity of our 

 datasets is demonstrated by visualizing the geometries distribution with 

 dimensionality reduction as well as via comparison of statistical 

 features of the QM properties with those available in existing datasets. 

 Our sampling targets broader quantum mechanical distribution of the 

 configurational space than provided by commonly used sampling through 

 classical molecular dynamics, upping the challenge for machine learning 

 models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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{https://doi.org/10.1002/bimj.202100210,

title = {Correcting for heterogeneity and non-comparability bias in multicenter clinical trials with a rescaled random-effect excess hazard model},

author = {Juste A. Goungounga and Nathalie Grafféo and Hadrien Charvat and Roch Giorgi},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bimj.202100210},

doi = {https://doi.org/10.1002/bimj.202100210},

year  = {2023},

date = {2023-01-01},

journal = {Biometrical Journal},

volume = {65},

number = {4},

pages = {2100210},

abstract = {Abstract In the presence of competing causes of event occurrence (e.g., death), the interest might not only be in the overall survival but also in the so-called net survival, that is, the hypothetical survival that would be observed if the disease under study were the only possible cause of death. Net survival estimation is commonly based on the excess hazard approach in which the hazard rate of individuals is assumed to be the sum of a disease-specific and expected hazard rate, supposed to be correctly approximated by the mortality rates obtained from general population life tables. However, this assumption might not be realistic if the study participants are not comparable with the general population. Also, the hierarchical structure of the data can induces a correlation between the outcomes of individuals coming from the same clusters (e.g., hospital, registry). We proposed an excess hazard model that corrects simultaneously for these two sources of bias, instead of dealing with them independently as before. We assessed the performance of this new model and compared it with three similar models, using extensive simulation study, as well as an application to breast cancer data from a multicenter clinical trial. The new model performed better than the others in terms of bias, root mean square error, and empirical coverage rate. The proposed approach might be useful to account simultaneously for the hierarchical structure of the data and the non-comparability bias in studies such as long-term multicenter clinical trials, when there is interest in the estimation of net survival.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WOS:001043129200034,

title = {When local alterations meet collective oscillatory dynamics: On the 

 causes of functional connectivity changes},

author = {Sophie Benitez Stulz and Matthieu Gilson and Demian Battaglia},

issn = {0929-5313},

year  = {2023},

date = {2023-01-01},

journal = {JOURNAL OF COMPUTATIONAL NEUROSCIENCE},

volume = {51},

number = {1},

pages = {S24},

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:000911523800003,

title = {An efficient electrostatic embedding QM/MM method using periodic 

 boundary conditions based on particle-mesh Ewald sums and electrostatic 

 potential fitted charge operators},

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

doi = {10.1063/5.0133646},

issn = {0021-9606},

year  = {2023},

date = {2023-01-01},

journal = {JOURNAL OF CHEMICAL PHYSICS},

volume = {158},

number = {2},

abstract = {Hybrid quantum mechanics/molecular mechanics (QM/MM) models are 

 successful at describing the properties and reactivity of biological 

 macromolecules. Combining ab initio QM/MM methods and periodic boundary 

 conditions (PBC) is currently the optimal approach for modeling chemical 

 processes in an infinite environment, but frequently, these models are 

 too time-consuming for general applicability to biological systems in a 

 solution. Here, we define a simple and efficient electrostatic embedding 

 QM/MM model in PBC, combining the benefits of electrostatic potential 

 fitted atomic charges and particle-mesh Ewald sums, which can 

 efficiently treat systems of an arbitrary size at a reasonable 

 computational cost. To illustrate this, we apply our scheme to extract 

 the lowest singlet excitation energies from a model for Arabidopsis 

 thaliana cryptochrome 1 containing circa 93 000 atoms, accurately 

 reproducing the experimental absorption maximum.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{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: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}

}