Multi-compartment poroelastic models of perfused biological soft tissues: implementation in FEniCSx

Soft biological tissues demonstrate strong time-dependent and strain-rate mechanical behavior, arising from their intrinsic visco-elasticity and fluid-solid interactions (especially at sufficiently large time scales). The time-dependent mechanical properties of soft tissues influence their physiological functions and are linked to several pathological processes. Poro-elastic modeling represents a promising approach because it allows the integration of multiscale/multiphysics data to probe biologically relevant phenomena at a smaller scale and embeds the relevant mechanisms at the larger scale. The implementation of multi-phasic flow poro-elastic models however is a complex undertaking, requiring extensive knowledge. The open-source software FEniCSx Project provides a novel tool for the automated solution of partial differential equations by the finite element method. This paper aims to provide the required tools to model the mixed formulation of poro-elasticity, from the theory to the implementation, within FEniCSx. Several benchmark cases are studied. A column under confined compression conditions is compared to the Terzaghi analytical solution, using the L2-norm. An implementation of poro-hyper-elasticity is proposed. A bi-compartment column is compared to previously published results (Cast3m implementation). For all cases, accurate results are obtained in terms of a normalized Root Mean Square Error (RMSE). Furthermore, the FEniCSx computation is found three times faster than the legacy FEniCS one. The benefits of parallel computation are also highlighted.Comment: https://github.com/Th0masLavigne/Dolfinx_Porous_Media.gi

Love Wave Propagation in Poro elasticity

It is observed that on similar reasons as in classical theory of elasticity, SH wave propagation in a semi infinite poroelastic body is not possible and is possible when there is a layer of another poro elastic medium over it i.e., Love waves. Two particular cases are considered in one of which phase velocity can be determined for a given wave length. In the same case, equation for phase velocity is of the same form as that of the classical theory of Elasticity

Coupling of flow, contact mechanics and friction, generating waves in a fractured porous medium

We present a mixed dimensional model for a fractured poro-elasic medium including contact mechanics. The fracture is a lower dimensional surface embedded in a bulk poro-elastic matrix. The flow equation on the fracture is a Darcy type model that follows the cubic law for permeability. The bulk poro-elasticity is governed by fully dynamic Biot equations. The resulting model is a mixed dimensional type where the fracture flow on a surface is coupled to a bulk flow and geomechanics model. The particularity of the work here is in considering fully dynamic Biot equation, that is, including an inertia term, and the contact mechanics including friction for the fracture surface. We prove the well-posedness of the continuous model

Finite-strain poro-visco-elasticity with degenerate mobility

A quasistatic nonlinear model for poro-visco-elastic solids at finite strains is considered in the Lagrangian frame using the concept of second-order nonsimple materials. The elastic stresses satisfy static frame-indifference, while the viscous stresses satisfy dynamic frame-indifference. The mechanical equation is coupled to a diffusion equation for a solvent or fluid content. The latter is pulled-back to the reference configuration. To treat the nonlinear dependence of the mobility tensor on the deformation gradient, the result by Healey & Krömer is used to show that the determinant of the deformation gradient is bounded away from zero. Moreover, the focus is on the physically relevant case of degenerate mobilities. The existence of weak solutions is shown using a staggered time-incremental scheme and suitable energy-dissipation inequalities

The role of structural viscoelasticity in deformable porous media with incompressible constituents: applications in biomechanics

The main goal of this work is to clarify and quantify, by means of mathematical analysis, the role of structural viscoelasticity in the biomechanical response of deformable porous media with incompressible constituents to sudden changes in external applied loads. Models of deformable porous media with incompressible constituents are often utilized to describe the behavior of biological tissues, such as cartilages, bones and engineered tissue scaffolds, where viscoelastic properties may change with age, disease or by design. Here, for the first time, we show that the fluid velocity within the medium could increase tremendously, even up to infinity, should the external applied load experience sudden changes in time and the structural viscoelasticity be too small. In particular, we consider a one-dimensional poro-visco-elastic model for which we derive explicit solutions in the cases where the external applied load is characterized by a step pulse or a trapezoidal pulse in time. By means of dimensional analysis, we identify some dimensionless parameters that can aid the design of structural properties and/or experimental conditions as to ensure that the fluid velocity within the medium remains bounded below a certain given threshold, thereby preventing potential tissue damage. The application to confined compression tests for biological tissues is discussed in detail. Interestingly, the loss of viscoelastic tissue properties has been associated with various disease conditions, such as atherosclerosis, Alzheimer's disease and glaucoma. Thus, the findings of this work may be relevant to many applications in biology and medicine

Temperature induced pore fluid pressurization in geomaterials

The theoretical basis of the thermal response of the fluid-saturated porous materials in undrained condition is presented. It has been demonstrated that the thermal pressurization phenomenon is controlled by the discrepancy between the thermal expansion of the pore fluid and of the solid phase, the stress-dependency of the compressibility and the non-elastic volume changes of the porous material. For evaluation of the undrained thermo-poro-elastic properties of saturated porous materials in conventional triaxial cells, it is important to take into account the effect of the dead volume of the drainage system. A simple correction method is presented to correct the measured pore pressure change and also the measured volumetric strain during an undrained heating test. It is shown that the porosity of the tested material, its drained compressibility and the ratio of the volume of the drainage system to the one of the tested sample, are the key parameters which influence the most the error induced on the measurements by the drainage system. An example of the experimental evaluation of undrained thermoelastic parameters is presented for an undrained heating test performed on a fluid-saturated granular rock

Stress dependent thermal pressurization of a fluid-saturated rock

Temperature increase in saturated porous materials under undrained conditions leads to thermal pressurization of the pore fluid due to the discrepancy between the thermal expansion coefficients of the pore fluid and of the solid matrix. This increase in the pore fluid pressure induces a reduction of the effective mean stress and can lead to shear failure or hydraulic fracturing. The equations governing the phenomenon of thermal pressurization are presented and this phenomenon is studied experimentally for a saturated granular rock in an undrained heating test under constant isotropic stress. Careful analysis of the effect of mechanical and thermal deformation of the drainage and pressure measurement system is performed and a correction of the measured pore pressure is introduced. The test results are modelled using a non-linear thermo-poro-elastic constitutive model of the granular rock with emphasis on the stress-dependent character of the rock compressibility. The effects of stress and temperature on thermal pressurization observed in the tests are correctly reproduced by the model