Yohan Davit

• CR at French National Centre for Scientific Research

Correction for ‘Functionality integration in stereolithography 3D printed microfluidics using a “print-pause-print” strategy’ by Matthieu Sagot et al. , Lab Chip , 2024, 24 , 3508–3520, https://doi.org/10.1039/D4LC00147H.

The vast majority of bacteria live in sessile biofilms that colonize the channels, pores and crevices of confined structures. Flow in these structures carries the nutrients necessary for growth, but also generates stresses and detachment from surfaces. Conversely, bacteria tend to occupy a large part of the available space and, in so doing, increas...

The vast majority of bacteria live in sessile biofilms that colonize the channels, pores and crevices of confined structures. Flow in these structures carries the nutrients necessary for growth, but also generates stresses and detachment from surfaces. Conversely, bacteria tend to occupy a large part of the available space and, in so doing, increas...

Novel protocol for integration of object inside stereolithography-based chips and proof-of-concepts: bacteria imaging, blue energy and in-flow cell capture.

The vast majority of bacteria live in sessile biofilms that colonize the channels, pores and crevices of confined structures. Flow in these structures carries the nutrients necessary for growth, but also generates stresses and detachment from surfaces. Conversely, bacteria tend to occupy a large part of the available space and, in so doing, increas...

Recent progresses in intravital imaging have enabled highly-resolved measurements of periarteriolar oxygen gradients (POGs) within the brain parenchyma. POGs are increasingly used as proxies to estimate the local baseline oxygen consumption, which is a hallmark of cell activity. However, the oxygen profile around a given arteriole arises from an in...

Classical macro-scale dispersion equation cannot correctly represent non-local, non-equilibrium effects, and alternatives had to be proposed to overcome these discrepancies. Two-equation models have been widely used and proved useful to incorporate, to some extent, local non-equilibrium effects. More accurate descriptions may be obtained through th...

Recent microfluidic experiments have evidenced complex spatio-temporal fluctuations in low-Reynolds-number flows of polymer solutions through lattices of obstacles. However, understanding the nonlinear physics of such systems remains a challenge. Here, we use high performance simulations to study viscoelastic flows through a hexagonal lattice of cy...

We present a novel micromodel technology to explore bacterial biofilm development in porous media flows and demonstrate how it can be used to study the growth/detachment dynamics of Pseudomonas aeruginosa .

Polydimethylsiloxane (PDMS) microfluidic systems have been instrumental in better understanding couplings between physical mechanisms and bacterial biofilm processes, such as hydrodynamic effects. However, precise control of the growth conditions, for example, the initial distribution of cells on the substrate or the boundary conditions in a flow s...

Permafrost covers a quarter of northern hemisphere lands and is highly sensitive to climate warming. The role of hydrological drains and thermal insulators of the moss and lichen layers, which are the most widespread vegetation covers on tundra and taïga ecosystems, is largely acknowledged to be of primary importance for permafrost dynamics but is...

We develop a numerical scheme for the flow of viscoelastic fluids, including the OldroydB and FENE-CR constitutive models. The space discretization is staggered, using either the Marker-And-Cell (MAC) scheme for structured nonuniform grids, or the Rannacher and Turek (RT) nonconforming low-order finite element approximation for general quandrangula...

The flow of polymer solutions past solid obstacles or through porous media gives rise to rich physical phenomena over a wide range of spatial and temporal scales. Viscoelasticity, in particular, can induce a strong nonlinear response with an increase of flow resistance even for a solution whose viscosity decreases in simple shear flow. Various hypo...

Viscoelastic flows of polymer solutions in complex geometries can generate a strong localization of stress within small regions of the fluid and the formation of birefringent strands. In porous media, these localized structures of stress drive preferential flow paths and increase global dissipation. Modeling the impact of such effects at Darcy or l...

The flow of Dense Non-Aqueous Phase Liquid (DNAPL) in highly permeable porous media is characterized by a complex interplay between surface tension, viscous, gravity, and inertia forces. Gravitational effects in these systems have been particularly studied in the context of displacement instability, but little work has focused on the impact of grav...

To macroscopically describe two-phase flows in porous media, we need accurate modeling of the drag forces between the two fluids and the solid phase. In low-permeability porous media, where capillarity is often dominant, momentum exchange is often neglected and the fluid-fluid drag force is treated as part of the drag between fluids and solid in th...

The physics of blood flow in small vessel networks is dominated by the interactions between Red Blood Cells (RBCs), plasma and blood vessel walls. The resulting couplings between the microvessel network architecture and the heterogeneous distribution of RBCs at network-scale are still poorly understood. The main goal of this paper is to elucidate h...

Tit-for-tat is a familiar principle from animal behavior: individuals respond in kind to being helped or harmed by others. Remarkably some bacteria appear to display tit-for-tat behavior, but how this evolved is not understood. Here we combine evolutionary game theory with agent-based modelling of bacterial tit-for-tat, whereby cells stab rivals wi...

In this paper, we develop a numerical scheme for the solution of the coupled Stokes and Navier-Stokes equations with constitutive equations describing the flow of viscoelastic fluids. The space discretization is based on the so-called Marker-And-Cell (MAC) scheme. The time discretization uses a fractional-step algorithm where the solution of the Na...

Modelling solute transport in the brain microcirculation: is it really well mixed inside the blood vessels? - Volume 884 - Maxime Berg, Yohan Davit, Michel Quintard, Sylvie Lorthois

Modeling scalar transport by advection and diffusion in multiscale porous structures is a challenging problem, particularly in the preasymptotic regimes when non-Fickian effects are prominent. Mathematically, one of the main difficulties is to obtain macroscale models from the homogenization of conservation equations at microscale when epsilon, the...

The risk of dust explosion appears in many industrial situations. In nuclear safety analysis, one of the scenarios is the risk of graphite dust explosion that may occur during decommissioning operations of UNGG reactors [6]. In such a case, the problem is considered as a dispersed two-phase flow with particle size typically ranging from 1 to 100 µm...

CATHARE is a 2-fluid thermal-hydraulic system code, capable of simulating phenomena occurring in the primary and secondary circuits of a PWR (Pressurized Water Reactor) under a wide variety of accidental situations. The latest version CATHARE-3 uses a 3D modeling of a PWR core at the assembly scale to simulate various accidental situations such as...

Heat transfers in dilute gas-particle mixtures are often modeled using hybrid Euler–Lagrange descriptions, treating the carrier fluid via an Eulerian representation and following each particle in a Lagrangian framework. One of the focal issues in these models is the calculation of the macro-scale heat transfer between the continuous phase and parti...

Cerebral blood flow (CBF) reductions in Alzheimer’s disease patients and related mouse models have been recognized for decades, but the underlying mechanisms and resulting consequences for Alzheimer’s disease pathogenesis remain poorly understood. In APP/PS1 and 5xFAD mice we found that an increased number of cortical capillaries had stalled blood...

Despite the key role of the capillaries in neurovascular function, a thorough characterization of cerebral capillary network properties is currently lacking. Here, we define a range of metrics (geometrical, topological, flow, mass transfer, and robustness) for quantification of structural differences between brain areas, organs, species, or patient...

Fluid flows through porous media are subject to different regimes, ranging from linear creeping flows to unsteady, chaotic turbulence. These different flow regimes at the pore scale have repercussions at larger scales, with the macroscale drag force experienced by a fluid moving through the medium becoming a nonlinear function of the average veloci...

The risk of dust explosion appears in many industrial situations. In nuclear safety analysis, one of the scenarios is the risk of graphite dust explosion that may occur during decommissioning operations of UNGG reactors [6]. In such a case, the problem is considered as a dispersed two-phase flow with particle size typically ranging from 1 to 100 µm...

Modeling the flow of fluids with shear-dependent viscosity through porous media is a challenging fundamental and engineering problem. At continuum-scale, such flows are usually described using modified versions of Darcy’s law, which are obtained by considering either an apparent viscosity or an apparent permeability. In the two cases, Darcy’s law b...

Optical imaging techniques for biofilm observation, like laser scanning microscopy, are not applicable when investigating biofilm formation in opaque porous media. X-ray micro-tomography (X-ray CMT) might be an alternative but it finds limitations in similarity of X-ray absorption coefficients for the biofilm and aqueous phases. To overcome this di...

We explore how X-ray computed microtomography can be used to generate highly-resolved 3D biofilm datasets on length scales that span multiple pore bodies. The data is integrated into a study of the effects of flow rate on three-dimensional growth of biofilm in porous media. Three flow rates were investigated in model packed-bed columns. Biofilm gro...

Bacteria commonly live in dense and genetically diverse communities associated with surfaces. In these communities, competition for resources and space is intense, and yet we understand little of how this affects the spread of antibiotic-resistant strains. Here, we study interactions between antibiotic-resistant and susceptible strains using in vit...

Aging or cerebral diseases may induce architectural modifications in human brain microvascular networks, such as capillary rarefaction. Such modifications limit blood and oxygen supply to the cortex, possibly resulting in energy failure and neuronal death. Modelling is key in understanding how these architectural modifications affect blood flow and...

Comparison of the hybrid approach with reference complete network computations. In complete network version, arteriolar and venular trees are connected to 6- or 3-regular capillary networks. In the hybrid approach, they plunge into an equivalent porous medium which is discretized in finite volume cells of size h. (a) In configuration i, a single co...

Comparison of hybrid and reference CN approaches for the Baseline configuration displayed in Fig 6i(a). Here, a simple condition of pressure continuity is imposed at the interface between the arteriolar vessel and the continuum. (a) Global pressure errors. Global pressure errors are computed in the four domains of interest defined in 3(d). The erro...

Comparison of pressure profiles computed via hybrid and CN approaches, the hybrid approach being associated to a simple condition of pressure continuity at the coupling point. The pressure profile is plotted for a single centered coupling, as in Fig 6i(a) in the main paper. The reference pressure field from CN approach is represented by orange cros...

2D schematic diagrams of the distribution of the coupling condition for off-centered coupling point. To take into account the off-centering of a given coupling point s (red dot), the corresponding flow rate qs is distributed among each cell i of ΩFV,neighs (yellow hatching) according to the partition coefficient τi = vi/h3, where vi is the intersec...

Comparison between the hybrid and complete network approaches in a larger realistic configuration. Pressure and flow rate values are compared in a log-log plot. Black crosses refer to the hybrid approach using our coupling model. Gray crosses refer to the hybrid approach using a simple condition of pressure continuity at the interface between arter...

Global pressure and flow rate errors for multiple couplings occuring in the same FV cell. From 2 to 10 arteriolar and venular vessels are randomly coupled to a 6-regular capillary network, in such a way that they are located in the same FV cell in the FV domain of the equivalent hybrid configuration. According to physiological statistics (Fig 2(b))...

Scale differences between oil reservoirs and the human cortex. Three characteristic length scales are presented for both petroleum and cerebral applications: the pore size of the porous medium (oil reservoir or capillary bed), the diameter of the coupled component (wellbore or arteriolar/venular vessel) and the typical size of a discretization cell...

In this paper, a macro-scale model is proposed to describe heat transfer in a dilute gas-particle mixture. The continuous phase is described by a filtered Eulerian approach while the dispersed one is represented as Lagrangian particles. The filtered model, which is obtained using an up-scaling methodology, consists of a macroscopic heat transfer mo...

The existence of cerebral blood flow (CBF) reductions in Alzheimers disease (AD) patients and related mouse models has been known for decades, but the underlying mechanisms and the resulting impacts on cognitive function and AD pathogenesis remain poorly understood. In the APP/PS1 mouse model of AD we found that an increased number of cortical capi...

Continuum models that describe two-phase flow of immiscible fluids in porous media often treat momentum exchange between the two phases by simply generalizing the single-phase Darcy law and introducing saturation-dependent permeabilities. Here we study models of creeping flows that include an explicit coupling between both phases via the addition o...

A presentation I made as I was a PhD candidate at IMFT.

This paper is a first of a series aiming at revisiting technical aspects of the volume averaging theory. Here, we discuss the choice of the spatial averaging operator for periodic and quasiperiodic structures. We show that spatial averaging must be defined in terms of a convolution and analyze the properties of a variety of kernels, with a particul...

The flow of polymer solutions in porous media is often described using Darcy’s law with an apparent viscosity capturing the observed thinning or thickening effects. While the macroscale form is well accepted, the fundamentals of the pore-scale mechanisms, their link with the apparent viscosity, and their relative influence are still a matter of deb...

Bacteria interact in dense ecological networks of strains and species. The most obvious difference between many species is cell shape, and yet we understand little of how cell shape impacts the ecology and evolution of microbial communities. To address this, we combine a new individual-based model with experiments, competing microbial strains of di...

two-phase flow porous media, highly permeable structures

non-Fickian transport, multi-rate mass transfer, domain decomposition, volume averaging

Understanding and modeling flows in columns equipped with structured packings is crucial to enhance the efficiency of many processes in chemical engineering. As in most porous media, an important factor that affects the flow is the presence of rough surfaces, whether this roughness has been engineered as a texture on the corrugated sheets or is the...

Many industrial and natural processes involve flow in highly permeable media, such as exchangers, canopies, urban canyons. Traditional assumptions used for modeling flow equations in low permeability structures may not hold for these systems with very large pores. Reynolds numbers may be too large so that Darcy's law is no longer valid. Large Capil...

Significance Microbial communities contain cells of different shapes, and yet we know little about how these shapes affect community biology. We have developed a computational model to study the effects of microbial shape in communities. Our model predicts that shape will have strong effects on cells’ positioning, and, consequently, their survival...

Talk given at ECMOR XV.

Over the last decades, the intensive use of polymer mixtures in Enhanced Oil Recovery (EOR) has led to a great effort in understanding the flow of such fluids through complex porous media. While the macro-scale behavior of these fluids has been actively investigated using core-scale experiments, the link with the micro-scale fundamental physics of...

We use computational fluid dynamics to explore the creeping flow of power-law fluids through isotropic porous media. We find that the flow pattern is primarily controlled by the geometry of the porous structure rather than by the nonlinear effects in the rheology of the fluid. We further highlight a macroscale transition between a Newtonian and a n...

Columns containing structured packings play an important role in chemical engineering processes involving distillation and gas-liquid separation, such as air distillation or CO 2 absorption. The packings often consist of corrugated plates that significantly increase the exchange surface between gas and liquid phases in the column. The columns are g...

A wide variety of techniques have been developed to homogenize transport equations in multiscale and multiphase systems. This has yielded a rich and diverse field, but has also resulted in the emergence of isolated scientific communities and disconnected bodies of literature. Here, our goal is to bridge the gap between formal multiscale asymptotics...

Biofilms are involved in several natural or engineered systems. Their presence within porous media can substantially affect the hydrodynamic and the transport process. In this work, considering a simple porous medium including a real biofilm structure, we describe a complete work-flow to numerically evaluate effective properties of the medium. We...

We develop a one-equation non-equilibrium model to describe the Darcy-scale transport of a solute undergoing biodegradation in porous media. Most of the mathematical models that describe the macroscale transport in such systems have been developed intuitively on the basis of simple conceptual schemes. There are two problems with such a heuristic an...

The development of new models of biological tissues that consider cells in a discrete manner is becoming increasingly popular as an alternative to continuum methods based on partial differential equations, although formal relationships between the discrete and continuum frameworks remain to be established. For crystal mechanics, the discrete-to-con...

3D off-lattice simulation coupled to PDE: 3D simulation of a tumour spheroid. A cross-section of a tumour spheroid is presented. Cell centres, nodes of a mesh, are represented by spherical shells and coloured according to the local oxygen concentration. Proliferation is dependent on oxygen, which diffuses and is taken up by cells in the spheroid, s...

3D off-lattice simulation confined to a 2D surface: small intestinal crypts and villus. Left: cells are labelled according to their ancestor cell; each crypt gives rise to a monoclonal population, with a multiclonal villus comprised of cells from each crypt. Right: the same simulation, here with cells labelled according to Delta levels (non-dimensi...

Cardiac electrophysiology: a re-entrant spiral wave. This figure displays the membrane voltage in a 2-D monodomain simulation using the Luo-Rudy 1991 action-potential model [50] with the modifications and protocol suggested in [49]. The simulation runs from to milliseconds. (MP4)

Further details on installation of Chaste and dependencies. (PDF)

Cardiac electromechanics in a ventricular wedge: simulation of electrical propagation and deformation. A stimulus is applied to the face at and the simulation runs until milliseconds. (MP4)

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been...

Many microorganisms live within surface-associated consortia, termed biofilms, that can form intricate porous structures interspersed with a network of fluid channels. In such systems, transport phenomena, including flow and advection, regulate various aspects of cell behavior by controlling nutrient supply, evacuation of waste products, and permea...

In this work, we study the transient behavior of homogenized models for solute transport in two-region porous media. We focus on the following three models: (1) a time non-local, two-equation model (2eq-nlt). This model does not rely on time constraints and, therefore, is particularly useful in the short-time regime, when the timescale of interest...

In a recent paper, Valdès-Parada and Alvarez-Ramirez [ Phys. Rev. E 84 031201 (2011)] used the technique of volume averaging to derive a “frequency-dependent” dispersion tensor, Dγ*, the goal of which is to describe solute transport in porous media undergoing periodic processes. We describe two issues related to this dispersion tensor. First, we de...

In soils and rivers subsurface, bacterial biofilms growth induce modifications of mass and momentum transport dynamics. Evidence for these modifications have been developed essentially by inspection, that is, observation of the reduction of hydraulic conductivity, permeability, changes in porosity and anomalous transport. Deeper understanding of th...

Cette thèse se propose d’examiner les phénomènes de transport dans des milieux poreux colonisés par des biofilms. Ces communautés sessiles se développent dans les sols, les roches souterraines, ou dans la zone hyporhéique et peuvent influencer significativement le transport de masse et de quantité de mouvement. Les biofilms modifient également très...

Microbial biofilms are observed in both natural and engineered subsurface environments and can dramatically alter the physical properties of porous media. Current understanding of biofilm formation and the associated impacts to structural and hydrodynamic properties of porous media are limited by our ability to observe changes to pore morphology in...

This paper deals with local non-equilibrium models for mass transport in dual-phase and dual-region porous media. The first contribution of this study is to formally prove that the time-asymptotic moments matching method applied to two-equation models is equivalent to a fundamental deterministic perturbation decomposition proposed in Quintard et al...

Biodegradation in porous media is most often the consequence of coupled transport phenomena in the presence of biofilms. The description of such transport problems involves different scales: the bacteria scale, the scale of a locally homogenized biofilm, heterogeneous biofilms at a scale lower than the pore‐scale, the pore‐scale problem, the Darcy‐...

In this work, we are interested in linking local non-equilibrium models for mass transport in porous media. First, we introduce the so called quasi-stationary tw-equation model and its fully transient version obtained through a particular memory function closure. Then, we propose another fundamental way to obtain non-equilibrium models using a spec...

The general problem of transport and reaction in multiphase porous media has been a subject of extensive studies during the last decades. For example, biologically mediated porous media have seen a long history of research from the environmental engineering point of view. Biofilms (aggregate of microorganisms coated in a polymer matrix generated by...

The effective viscosity of dilute and semi-dilute suspensions in a shear flow in a microfluidic configuration is studied numerically. The suspension is composed of monodisperse and non-Brownian hard spherical buoyant particles confined between two walls in a shear flow. An abrupt change of the viscosity behaviour occurs with strong confinements: wh...

In this work, we study experimentally and numerically the viscosity of non-brownian confined suspensions of hard spherical particles confined between two walls in a shear flow. By varying the wall-to-wall distance (gap), we show that the viscosity presents a remarkable behavior as a function of the confinement. A transition occurs from a 3D configu...

Role of intercations between benthic fauna and biofilm on bio-physical functioning of the hyporheic compartment: a column-modeling approach

We study numerically the properties of a one-equation non-equilibrium model for describing mass transport and biodegradation in porous media with biofilms (Poster).

Le terme générique ''biofilm'' désigne un agrégat de microorganismes (bactéries, algues, champignons, protozoaires) vivant en symbiose au sein d'une matrice protective constituée de substances polymériques extracellulaires. Ces biofilms se développent en milieux aqueux ou humides dans de nombreux systèmes industriels et écosystèmes. En particulier,...

Mass and momentum transport in biologically reactive porous media have been particularly examined within the context of bioremediation of the hyporheic compartment and especially of rivers subsurface. The reactive transport is mediated by micro-organisms (primarily bacteria, fungi, and algae) aggregated and coated within an extracellular polymeric...

Micro-organisms (primarily bacteria, fungi and algae), in wet or aqueous environments, tend to aggregate and grow on surfaces, embedded within extracellular polymeric substances (EPS). These sessile communities, usually called biofilms, are ubiquitous in industry, in medicine and natural environments. Within porous media, for example soils or river...