arXiv subjects

Ricardo Ruiz-Baier

Publications and source records attributed to Ricardo Ruiz-Baier.

At least 37 records · Page 2Linked to original sources

arXiv2025

Analysis and virtual element discretisation of a Stokes/Biot--Kirchhoff bulk--surface model

We analyse a coupled 3D-2D model with a free fluid governed by Stokes flow in the bulk and a poroelastic plate described by the Biot-Kirchhoff equations on the surface. Assuming the form of a double perturbed saddle-point problem, the unique solvability of the continuous formulation is proved using Fredholm's theory for compact operators and the Babuska--Brezzi approach for saddle-point problems with penalty. We propose a stable virtual element method, establishing a discrete inf-sup condition under a small mesh assumption through a Fortin interpolant that requires only $H^1$-regularity for the Stokes problem. We show the well-posedness of the monolithic discrete formulation and introduce an equivalent fixed-point approach employed at the implementation level. The optimal convergence of the method in the energy norm is proved theoretically and is also confirmed numerically via computational experiments. We demonstrate an application of the model and the proposed scheme in the simulation of immune isolation using encapsulation with silicon nanopore membranes.

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arXiv2025

A velocity-vorticity-pressure formulation for the steady Navier--Stokes--Brinkman--Forchheimer problem

The flow of incompressible fluid in highly permeable porous media in vorticity - velocity - Bernoulli pressure form leads to a double saddle-point problem in the Navier--Stokes--Brinkman--Forchheimer equations. The paper establishes, for small sources, the existence of solutions on the continuous and discrete level of lowest-order piecewise divergence-free Crouzeix--Raviart finite elements. The vorticity employs a vector version of the pressure space with normal and tangential velocity jump penalisation terms. A simple Raviart--Thomas interpolant leads to pressure-robust a priori error estimates. An explicit residual-based a posteriori error estimate allows for efficient and reliable a posteriori error control. The efficiency for the Forchheimer nonlinearity requires a novel discrete inequality of independent interest. The implementation is based upon a light-weight forest-of-trees data structure handled by a highly parallel set of adaptive mesh refining algorithms. Numerical simulations reveal robustness of the a posteriori error estimates and improved convergence rates by adaptive mesh-refining.

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arXiv2025

Semi and fully-discrete analysis of lowest-order nonstandard finite element methods for the biharmonic wave problem

This paper discusses lowest-order nonstandard finite element methods for space discretization and explicit and implicit schemes for time discretization of the biharmonic wave equation with clamped boundary conditions. A modified Ritz projection operator defined on $H^2_0(Ω)$ ensures error estimates under appropriate regularity assumptions on the solution. Stability results and error estimates of optimal order are established in suitable norms for the semidiscrete and explicit/implicit fully-discrete versions of the proposed schemes. Finally, we report on numerical experiments using explicit and implicit schemes for time discretization and Morley, discontinuous Galerkin, and {C$^0$ interior} penalty schemes for space discretization, that validate the theoretical error estimates.

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arXiv2025

Mixed virtual element methods for a stress-velocity-rotation formulation in viscoelasticity

In this paper we propose a new mixed virtual element formulation for the numerical approximation of viscoelasticity equations with weakly imposed stress symmetry. The governing equations use the Zener model and are expressed in terms of the principal unknowns of additively decomposed stress into elastic and internal viscoelastic contributions, while the rotation tensor and velocity act as Lagrange multipliers. The time discretisation uses Crank--Nicolson's scheme. We demonstrate the unique solvability of both semi-discrete and fully-discrete problems by leveraging the properties of suitable local projectors. Moreover, we establish optimal a priori error estimates for all variables that appear in the mixed formulation. To validate our theoretical findings, we present several representative numerical examples that also highlight the features of the proposed formulation.

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arXiv2025

Tree-based adaptive finite element methods for deformable image registration

In this work we propose an adaptive Finite Element Method (FEM) formulation for the Deformable Image Registration problem (DIR) together with a residual-based a posteriori error estimator, whose efficiency and reliability are theoretically established. This estimator is used to guide Adaptive Mesh Refinement and coarsening (AMR). The nonlinear Euler-Lagrange equations associated with the minimisation of the relevant functional are solved with a pseudo time-stepping fixed-point scheme which is further accelerated using Anderson Acceleration (AA). The efficient implementation of these solvers relies on an efficient adaptive mesh data structure based on forests-of-octrees endowed with space-filling-curves. Several numerical results illustrate the performance of the proposed methods applied to adaptive DIR in application-oriented problems.

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arXiv2025

Analysis of a finite element method for the Stokes--Poisson--Boltzmann equations

We define a finite element method for the coupling of Stokes and nonlinear Poisson--Boltzmann equations. The novelty in the formulation is that the coupling from the electric potential to the drag in the momentum balance is rewritten as a weighted advection term. Using Banach's contraction principle, the Babuška--Brezzi theory, and the Minty--Browder theorem, we show that the governing equations have a unique weak solution. We also show that the discrete problem is well-posed, establish Céa estimates, and derive convergence rates. We exemplify the properties of the proposed scheme via some numerical experiments showcasing convergence and applicability in the study of electro-osmotic flows in micro-channels.

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arXiv2025

Accurate stochastic simulation of nonlinear reactions between closest particles

We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction conditions of this kind are commonly used in particle-based simulations of chemical kinetics to mimic bimolecular reactions, those involving just two reactants, and have been extensively studied. The rate at which particles react within the system is determined by the reaction condition and particulate diffusion. In the bimolecular case, analytic relations exist between the reaction rate and the distance at which particles react allowing modellers to tune the rate of the reaction within their simulations by simply altering the reaction condition. However, generalising proximity-based reaction conditions to trimolecular reactions, those involving three particles, is more complicated because it requires understanding the distribution of the closest diffusing particle to a point in the vicinity of a spatially dependent absorbing boundary condition. We find that in this case the evolution of the system is described by a nonlinear partial integro-differential equation with no known analytic solution, which makes it difficult to relate the reaction rate to the reaction condition. To resolve this, we use singular perturbation theory to obtain a leading-order solution and show how to derive an approximate expression for the reaction rate. We then use finite element methods to quantify the higher-order corrections to this solution and the reaction rate, which are difficult to obtain analytically. Leveraging the insights gathered from this analysis, we demonstrate how to correct for the errors that arise from adopting the approximate expression for the reaction rate, enabling for the construction of more accurate particle-based simulations than previously possible.

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arXiv2025

A priori and a posteriori error bounds for the fully mixed FEM formulation of poroelasticity with stress-dependent permeability

We develop a family of mixed finite element methods for a model of nonlinear poroelasticity where, thanks to a rewriting of the constitutive equations, the permeability depends on the total poroelastic stress and on the fluid pressure and therefore we can use the Hellinger--Reissner principle with weakly imposed stress symmetry for Biot's equations. The problem is adequately structured into a coupled system consisting of one saddle-point formulation, one linearised perturbed saddle-point formulation, and two off-diagonal perturbations. This system's unique solvability requires assumptions on regularity and Lipschitz continuity of the inverse permeability, and the analysis follows fixed-point arguments and the Babuška--Brezzi theory. The discrete problem is shown uniquely solvable by applying similar fixed-point and saddle-point techniques as for the continuous case. The method is based on the classical PEERS$_k$ elements, it is exactly momentum and mass conservative, and it is robust with respect to the nearly incompressible as well as vanishing storativity limits. We derive a priori error estimates, we also propose fully computable residual-based a posteriori error indicators, and show that they are reliable and efficient with respect to the natural norms, and robust in the limit of near incompressibility. These a posteriori error estimates are used to drive adaptive mesh refinement. The theoretical analysis is supported and illustrated by several numerical examples in 2D and 3D.

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arXiv2025

New twofold saddle-point formulations for Biot poroelasticity with porosity-dependent permeability

We propose four-field and five-field Hu--Washizu-type mixed formulations for nonlinear poroelasticity -- a coupled fluid diffusion and solid deformation process -- considering that the permeability depends on a linear combination between fluid pressure and dilation. As the determination of the physical strains is necessary, the first formulation is written in terms of the primal unknowns of solid displacement and pore fluid pressure as well as the poroelastic stress and the infinitesimal strain, and it considers strongly symmetric Cauchy stresses. The second formulation imposes stress symmetry in a weak sense and it requires the additional unknown of solid rotation tensor. We study the unique solvability of the problem using the Banach fixed-point theory, properties of twofold saddle-point problems, and the Banach--Nečas--Babuška theory. We propose monolithic Galerkin discretisations based on conforming Arnold--Winther for poroelastic stress and displacement, and either PEERS or Arnold--Falk--Winther finite element families for the stress-displacement-rotation field variables. The wellposedness of the discrete problem is established as well, and we show a priori error estimates in the natural norms. Some numerical examples are provided to confirm the rates of convergence predicted by the theory, and we also illustrate the use of the formulation in some typical tests in Biot poroelasticity.

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arXiv2024

Robust virtual element methods for coupled stress-assisted diffusion problems

This paper aims first to perform robust continuous analysis of a mixed nonlinear formulation for stress-assisted diffusion of a solute that interacts with an elastic material, and second to propose and analyse a virtual element formulation of the model problem. The two-way coupling mechanisms between the Herrmann formulation for linear elasticity and the reaction-diffusion equation (written in mixed form) consist of diffusion-induced active stress and stress-dependent diffusion. The two sub-problems are analysed using the extended Babuška--Brezzi--Braess theory for perturbed saddle-point problems. The well-posedness of the nonlinearly coupled system is established using a Banach fixed-point strategy under the smallness assumption on data. The virtual element formulations for the uncoupled sub-problems are proven uniquely solvable by a fixed-point argument in conjunction with appropriate projection operators. We derive the a priori error estimates, and test the accuracy and performance of the proposed method through computational simulations.

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arXiv2024

A Lagrange Multiplier-based method for Stokes-linearized poro-hyperelastic interface problems

We propose a model for the coupling between free fluid and a linearized poro-hyperelastic body. In this model, the Brinkman equation is employed for fluid flow in the porous medium, incorporating inertial effects into the fluid dynamics. A generalized poromechanical framework is used, incorporating fluid inertial effects in accordance with thermodynamic principles. We carry out the analysis of the unique solvability of the governing equations, and the existence proof relies on an auxiliary multi-valued parabolic problem. We propose a Lagrange multiplier-based mixed finite element method for its numerical approximation and show the well-posedness of both semi-and fully-discrete problems. Then, a priori error estimates for both the semi- and fully-discrete schemes are derived. A series of numerical experiments is presented to confirm the theoretical convergence rates, and we also employ the proposed monolithic scheme to simulate 2D physical phenomena in geophysical fluids and biomechanics of the brain function.

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arXiv2024

Numerical analysis of a porous natural convection system with vorticity and viscous dissipation

In this paper we propose and analyse a new formulation and pointwise divergence-free mixed finite element methods for the numerical approximation of Darcy--Brinkman equations in vorticity--velocity--pressure form, coupled with a transport equation for thermal energy with viscous dissipative effect and mixed Navier-type boundary conditions. The solvability analysis of the continuous and discrete problems is significantly more involved than usual as it hinges on Banach spaces needed to properly control the advective and dissipative terms in the non-isothermal energy balance equation. We proceed by decoupling the set of equations and use the Banach fixed-point theorem in combination with the abstract theory for perturbed saddle-point problems. Some of the necessary estimates are straightforward modifications of well-known results, while other technical tools require a more elaborated analysis. The velocity is approximated by Raviart--Thomas elements, the vorticity uses Nédélec spaces of the first kind, the pressure is approximated by piecewise polynomials, and the temperature by continuous and piecewise polynomials of one degree higher than pressure. Special care is needed to establish discrete inf-sup conditions since the curl of the discrete vorticity is not necessarily contained in the discrete velocity space, therefore suggesting to use two different Raviart--Thomas interpolants. A discrete fixed-point argument is used to show well-posedness of the Galerkin scheme. Error estimates in appropriate norms are derived, and a few representative numerical examples in 2D and 3D and with mixed boundary conditions are provided.

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arXiv2024

Virtual element methods for Biot-Kirchhoff poroelasticity

This paper analyses conforming and nonconforming virtual element formulations of arbitrary polynomial degrees on general polygonal meshes for the coupling of solid and fluid phases in deformable porous plates. The governing equations consist of one fourth-order equation for the transverse displacement of the middle surface coupled with a second-order equation for the pressure head relative to the solid with mixed boundary conditions. We propose novel enrichment operators that connect nonconforming virtual element spaces of general degree to continuous Sobolev spaces. These operators satisfy additional orthogonal and best-approximation properties (referred to as a conforming companion operator in the context of finite element methods), which play an important role in the nonconforming methods. This paper proves a priori error estimates in the best-approximation form, and derives residual--based reliable and efficient a posteriori error estimates in appropriate norms, and shows that these error bounds are robust with respect to the main model parameters. The computational examples illustrate the numerical behaviour of the suggested virtual element discretisations and confirm the theoretical findings on different polygonal meshes with mixed boundary conditions.

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arXiv2023

Robust finite element methods and solvers for the Biot--Brinkman equations in vorticity form

In this paper, we propose a new formulation and a suitable finite element method for the steady coupling of viscous flow in deformable porous media using divergence-conforming filtration fluxes. The proposed method is based on the use of parameter-weighted spaces, which allows for a more accurate and robust analysis of the continuous and discrete problems. Furthermore, we conduct a solvability analysis of the proposed method and derive optimal error estimates in appropriate norms. These error estimates are shown to be robust in the case of large Lamé parameters and small permeability and storativity coefficients. To illustrate the effectiveness of the proposed method, we provide a few representative numerical examples, including convergence verification, poroelastic channel flow simulation, and test the robustness of block-diagonal preconditioners with respect to model parameters.

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arXiv2023

Numerical solution of the Biot/elasticity interface problem using virtual element methods

We propose, analyze and implement a virtual element discretization for an interfacial poroelasticity-elasticity consolidation problem. The formulation of the time-dependent poroelasticity equations uses displacement, fluid pressure, and total pressure, and the elasticity equations are written in the displacement-pressure formulation. The construction of the virtual element scheme does not require Lagrange multipliers to impose the transmission conditions (continuity of displacement and total traction, and no-flux for the fluid) on the interface. We show the stability and convergence of the virtual element method for different polynomial degrees, and the error bounds are robust with respect to delicate model parameters (such as Lame constants, permeability, and storativity coefficient). Finally, we provide numerical examples that illustrate the properties of the scheme.

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arXiv2022

Coupling chemotaxis and growth poromechanics for the modelling of feather primordia patterning

We propose a new mathematical model for the interaction of skin cell populations with fibroblast growth factor and bone morphogenetic protein, occurring within deformable porous media. The equations for feather primordia pattering are based on the work by K.J. Painter et al. [J. Theoret. Biol., 437 (2018) 225--238]. We perform a linear stability analysis to identify relevant parameters in the coupling mechanisms, focusing in the regime of infinitesimal strains. We also extend the model to the case of nonlinear poroelasticity and include solid growth by means of Lee decompositions of the deformation gradient. We present a few illustrative computational examples in 2D and 3D, and briefly discuss the design of tailored efficient solvers.

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arXiv2022

On augmented finite element formulation for the Navier--Stokes equations with vorticity and variable viscosity

We propose and analyse an augmented mixed finite element method for the Navier--Stokes equations written in terms of velocity, vorticity, and pressure with non-constant viscosity and no-slip boundary conditions. The weak formulation includes least-squares terms arising from the constitutive equation and from the incompressibility condition. The theoretical and practical implications of using augmentation is discussed in detail. In addition, we use fixed--point strategies to show the existence and uniqueness of continuous and discrete solutions under the assumption of sufficiently small data. The method is constructed using any compatible finite element pair for velocity and pressure as dictated by Stokes inf-sup stability, while for vorticity any generic discrete space (of arbitrary order) can be used. We establish optimal a priori error estimates. Finally, we provide a set of numerical tests in 2D and 3D illustrating the behaviour of the scheme as well as verifying the theoretical convergence rates.

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arXiv2022

Finite element methods for large-strain poroelasticity/chemotaxis models simulating the formation of myocardial oedema

In this paper we propose a novel coupled poroelasticity-diffusion model for the formation of extracellular oedema and infectious myocarditis valid in large deformations, manifested as an interaction between interstitial flow and the immune-driven dynamics between leukocytes and pathogens. The governing partial differential equations are formulated in terms of skeleton displacement, fluid pressure, Lagrangian porosity, and the concentrations of pathogens and leukocytes. A five-field finite element scheme is proposed for the numerical approximation of the problem, and we provide the stability analysis for a simplified system emanating from linearisation. We also discuss the construction of an adequate, Schur complement based, nested preconditioner. The produced computational tests exemplify the properties of the new model and of the finite element schemes.

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