During early development of multi-cellular animals, cells self-organize to set up the body axes, such as the primary head-to-tail axis, based on which the later body plan is defined. Several signaling pathways are known to control body axis formation. Here, we show, however, that tissue mechanics plays an important role during this process. We focus on the emergence of a primary axis in initially spherical aggregates of mouse embryonic stem cells, which mirrors events in the early mouse embryo. These aggregates break rotational symmetry to establish an axial organization with domains of different expression profiles, e.g. of the transcription factor T/Bra and the adhesion molecule E-cadherin. Combining quantitative microscopy and physical modeling, we identify large-scale tissue flows with a recirculation component and demonstrate that they significantly contribute to symmetry breaking. We show that the recirculating flows are explained by a difference in tissue surface tension across domains, akin to Marangoni flows, which we further confirm by aggregate fusion experiments. Our work highlights that body axis formation is not only driven by biochemical processes, but that it can also be amplified by tissue flows. We expect this type of amplification to operate in many other organoid and in-vivo systems.
Olivier Mesdjian, Chenglei Wang, Simon Gsell, Umberto D’ortona, Julien Favier, et al.. Longitudinal to Transverse Metachronal Wave Transitions in an In Vitro Model of Ciliated Bronchial Epithelium. Physical Review Letters, 2022, 129 (3), pp.038101. ⟨10.1103/PhysRevLett.129.038101⟩. ⟨hal-03741505⟩ Plus de détails...
Olivier Mesdjian, Chenglei Wang, Simon Gsell, Umberto D’ortona, Julien Favier, et al.. Longitudinal to Transverse Metachronal Wave Transitions in an In Vitro Model of Ciliated Bronchial Epithelium. Physical Review Letters, 2022, 129 (3), pp.038101. ⟨10.1103/PhysRevLett.129.038101⟩. ⟨hal-03741505⟩
The boundary slip error resulting from the interpolation/spreading non-reciprocity of the direct-forcing immersedboundary method is analyzed based on a simple and generic theoretical framework. In explicit implementations, the slip error scales with the Courant number, as predicted by the analysis and confirmed by lattice-Boltzmann simulation results. Using an analytical approximation of the non-reciprocity error, the immersed-boundary force can be corrected in order to prevent boundary slip and flow penetration. This a priori correction leads to a major improvement of the no-slip condition while avoiding any additional computational time or implementation effort.
Simon Gsell, Julien Favier. Direct-forcing immersed-boundary method: a simple correction preventing boundary slip error. Journal of Computational Physics, 2021, 435, pp.110265. ⟨10.1016/j.jcp.2021.110265⟩. ⟨hal-03425864⟩
Simon Gsell, Umberto d'Ortona, Julien Favier. Lattice-Boltzmann simulation of creeping generalized Newtonian flows: theory and guidelines. Journal of Computational Physics, 2021, 429, pp.109943. ⟨10.1016/j.jcp.2020.109943⟩. ⟨hal-03166492⟩ Plus de détails...
The accuracy of the lattice-Boltzmann (LB) method is related to the relaxation time controlling the flow viscosity. In particular, it is often recommended to avoid large fluid viscosities in order to satisfy the low-Knudsen-number assumption that is essential to recover hydrodynamic behavior at the macroscopic scale, which may in principle limit the possibility of simulating creeping flows and non-Newtonian flows involving important viscosity variations. Here it is shown, based on the continuous Boltzmann equations, that a two-relaxation-time (TRT) model can however recover the steady Navier-Stokes equations without any restriction on the fluid viscosity, provided that the Knudsen number is redefined as a function of both relaxation times. This effective Knudsen number is closely related to the previously-described parameter controlling numerical errors of the TRT model, providing a consistent theory at both the discrete and continuous levels. To simulate incompressible flows, the viscous incompressibility condition M a 2 /Re 1 also needs to be satisfied, where M a and Re are the Mach and Reynolds numbers. This concept is extended by defining a local incompressibility factor, allowing one to locally control the accuracy of the simulation for flows involving varying viscosities. These theoretical arguments are illustrated based on numerical simulations of the two-dimensional flow past a square cylinder. In the case of a Newtonian flow, the viscosity independence is confirmed for relaxation times up to 10 4 , and the ratio M a 2 /Re = 0.1 is small enough to ensure reliable incompressible simulations. The Herschel-Bulkley model is employed to introduce shear-dependent viscosities in the flow. The proposed numerical strategy allows to achieve major viscosity variations, avoiding the implementation of artificial viscosity cutoff in high-viscosity regions. Highly non-linear flows are simulated over ranges of the Bingham number Bn ∈ [1, 1000] and flow index n ∈ [0.2, 1.8], and successfully compared to prior numerical works based on Navier-Stokes solvers. This work provides a general framework to simulate complex creeping flows, as encountered in many biological and industrial systems, using the lattice-Boltzmann method.
Simon Gsell, Umberto d'Ortona, Julien Favier. Lattice-Boltzmann simulation of creeping generalized Newtonian flows: theory and guidelines. Journal of Computational Physics, 2021, 429, pp.109943. ⟨10.1016/j.jcp.2020.109943⟩. ⟨hal-03166492⟩
Etienne Loiseau, Simon Gsell, Aude Nommick, Charline Jomard, Delphine Gras, et al.. Active mucus–cilia hydrodynamic coupling drives self-organization of human bronchial epithelium. Nature Physics, 2020, ⟨10.1038/s41567-020-0980-z⟩. ⟨hal-02914172⟩ Plus de détails...
The respiratory tract is protected by mucus, a complex fluid transported along the epithelial surface by the coordinated beating of millions of microscopic cilia, hence the name of mucociliary clearance. Its impairment is associated with all severe chronic respiratory diseases. Yet, the relationship between ciliary density and the spatial scale of mucus transport, as well as the mechanisms that drive ciliary-beat orientations are much debated. Here, we show on polarized human bronchial epithelia that mucus swirls and circular orientational order of the underlying ciliary beats emerge and grow during ciliogenesis, until a macroscopic mucus transport is achieved for physiological ciliary densities. By establishing that the macroscopic ciliary-beat order is lost and recovered by removing and adding mucus, respectively, we demonstrate that cilia–mucus hydrodynamic interactions govern the collective dynamics of ciliary-beat directions. We propose a two-dimensional model that predicts a phase diagram of mucus transport in accordance with the experiments. This paves the way to a predictive in silico modelling of bronchial mucus transport in health and disease.
Etienne Loiseau, Simon Gsell, Aude Nommick, Charline Jomard, Delphine Gras, et al.. Active mucus–cilia hydrodynamic coupling drives self-organization of human bronchial epithelium. Nature Physics, 2020, ⟨10.1038/s41567-020-0980-z⟩. ⟨hal-02914172⟩
Simon Gsell, Etienne Loiseau, Umberto D’ortona, Annie Viallat, Julien Favier. Hydrodynamic model of directional ciliary-beat organization in human airways. Scientific Reports, 2020, 10 (8405), ⟨10.1038/s41598-020-64695-w⟩. ⟨hal-02614711⟩ Plus de détails...
In the lung, the airway surface is protected by mucus, whose transport and evacuation is ensured through active ciliary beating. the mechanisms governing the long-range directional organization of ciliary beats, required for effective mucus transport, are much debated. Here, we experimentally show on human bronchial epithelium reconstituted in-vitro that the dynamics of ciliary-beat orientation is closely connected to hydrodynamic effects. To examine the fundamental mechanisms of this self-organization process, we build a two-dimensional model in which the hydrodynamic coupling between cilia is provided by a streamwise-alignment rule governing the local orientation of the ciliary forcing. The model reproduces the emergence of the mucus swirls observed in the experiments. The predicted swirl sizes, which scale with the ciliary density and mucus viscosity, are in agreement with in-vitro measurements. A transition from the swirly regime to a long-range unidirectional mucus flow allowing effective clearance occurs at high ciliary density and high mucus viscosity. In the latter case, the mucus flow tends to spontaneously align with the bronchus axis due to hydrodynamic effects.
Simon Gsell, Etienne Loiseau, Umberto D’ortona, Annie Viallat, Julien Favier. Hydrodynamic model of directional ciliary-beat organization in human airways. Scientific Reports, 2020, 10 (8405), ⟨10.1038/s41598-020-64695-w⟩. ⟨hal-02614711⟩
The lattice Boltzmann method often involves small numerical time steps due to the acoustic scaling (i.e., scaling between time step and grid size) inherent to the method. In this work, a second-order dual-time-stepping lattice Boltzmann method is proposed in order to avoid any time-step restriction. The implementation of the dual time stepping is based on an external source in the lattice Boltzmann equation, related to the time derivatives of the macroscopic flow quantities. Each time step is treated as a pseudosteady problem. The convergence rate of the steady lattice Boltzmann solver is improved by implementing a multigrid method. The developed solver is based on a two-relaxation time model coupled to an immersed-boundary method. The reliability of the method is demonstrated for steady and unsteady laminar flows past a circular cylinder, either fixed or towed in the computational domain. In the steady-flow case, the multigrid method drastically increases the convergence rate of the lattice Boltzmann method. The dual-time-stepping method is able to accurately reproduce the unsteady flows. The physical time step can be freely adjusted; its effect on the simulation cost is linear, while its impact on the accuracy follows a second-order trend. Two major advantages arise from this feature. (i) Simulation speed-up can be achieved by increasing the time step while conserving a reasonable accuracy. A speed-up of 4 is achieved for the unsteady flow past a fixed cylinder, and higher speed-ups are expected for configurations involving slower flow variations. Significant additional speed-up can also be achieved by accelerating transients. (ii) The choice of the time step allows us to alter the range of simulated timescales. In particular, increasing the time step results in the filtering of undesired pressure waves induced by sharp geometries or rapid temporal variations, without altering the main flow dynamics. These features may be critical to improve the efficiency and range of applicability of the lattice Boltzmann method.
Simon Gsell, Umberto d'Ortona, Julien Favier. Multigrid dual-time-stepping lattice Boltzmann method. Physical Review E , 2020, 101 (2), ⟨10.1103/PhysRevE.101.023309⟩. ⟨hal-02573156⟩
Simon Gsell, Umberto d'Ortona, Julien Favier. Explicit and viscosity-independent immersed-boundary scheme for the lattice Boltzmann method. Physical Review E , 2019, 100 (3), ⟨10.1103/PhysRevE.100.033306⟩. ⟨hal-02339475⟩ Plus de détails...
Viscosity independence of lattice-Boltzmann methods is a crucial issue to ensure the physical relevancy of the predicted macroscopic flows over large ranges of physical parameters. The immersed-boundary (IB) method, a powerful tool that allows one to immerse arbitrary-shaped, moving, and deformable bodies in the flow, suffers from a boundary-slip error that increases as a function of the fluid viscosity, substantially limiting its range of application. In addition, low fluid viscosities may result in spurious oscillations of the macroscopic quantities in the vicinity of the immersed boundary. In this work, it is shown mathematically that the standard IB method is indeed not able to reproduce the scaling properties of the macroscopic solution, leading to a viscosity-related error on the computed IB force. The analysis allows us to propose a simple correction of the IB scheme that is local, straightforward and does not involve additional computational time. The derived method is implemented in a two-relaxation-time D2Q9 lattice-Boltzmann solver, applied to several physical configurations, namely, the Poiseuille flow, the flow around a cylinder towed in still fluid, and the flow around a cylinder oscillating in still fluid, and compared to a noncorrected immersed-boundary method. The proposed correction leads to a major improvement of the viscosity independence of the solver over a wide range of relaxation times (from 0.5001 to 50), including the correction of the boundary-slip error and the suppression of the spurious oscillations. This improvement may considerably extend the range of application of the IB lattice-Boltzmann method, in particular providing a robust tool for the numerical analysis of physical problems involving fluids of varying viscosity interacting with solid geometries.
Simon Gsell, Umberto d'Ortona, Julien Favier. Explicit and viscosity-independent immersed-boundary scheme for the lattice Boltzmann method. Physical Review E , 2019, 100 (3), ⟨10.1103/PhysRevE.100.033306⟩. ⟨hal-02339475⟩
Simon Gsell, Rémi Bourguet, Marianna Braza. One- versus two-degree-of-freedom vortex-induced vibrations of a circular cylinder at Re=3900. Journal of Fluids and Structures, 2019, 85, pp.165-180. ⟨10.1016/j.jfluidstructs.2019.01.006⟩. ⟨hal-02062155⟩ Plus de détails...
The one- versus two-degree-of-freedom vortex-induced vibrations of a circular cylinder are investigated on the basis of direct numerical simulation results. The Reynolds number, based on the oncoming flow velocity and cylinder diameter, is set to 3900. Three cases are examined: the elastically mounted body is free to oscillate either in the direction aligned with the current (in-line direction; IL case), in the direction normal to the current (cross-flow direction; CF case), or in both directions (IL+CF case). In each case, the behavior of the flow–structure system is studied over a range of values of the reduced velocity (inverse of the oscillator natural frequency). The in-line and cross-flow responses observed in the IL+CF case substantially differ from their one-degree-of-freedom counterparts, especially in the intermediate reduced velocity region. In this region, no vibrations develop in the IL case and in-line oscillations only occur if cross-flow motion is allowed. These in-line oscillations are accompanied by a major increase of the cross-flow responses, compared to the CF case. The two-degree-of-freedom vibrations are associated with the emergence of large-amplitude higher harmonics in the fluid force spectra. These aspects and more specifically the impact of the existence of a degree-of-freedom and oscillations in a given direction, on the fluid force and structural response in the perpendicular direction, do not seem to be systematically connected to changes in wake topology. Here, they are discussed in light of the orientation and magnitude of the instantaneous flow velocity seen by the moving body.
Simon Gsell, Rémi Bourguet, Marianna Braza. One- versus two-degree-of-freedom vortex-induced vibrations of a circular cylinder at Re=3900. Journal of Fluids and Structures, 2019, 85, pp.165-180. ⟨10.1016/j.jfluidstructs.2019.01.006⟩. ⟨hal-02062155⟩
