New preprint on mixed finite elements for multiple-network poroelasticity available!

Our new paper on A mixed finite element method for nearly incompressible multiple-network poroelasticity is now available on arXiv!

In this paper, we present and analyze a new mixed finite element formulation of a general family of quasi-static multiple-network poroelasticity (MPET) equations. The MPET equations describe flow and deformation in an elastic porous medium that is permeated by multiple fluid networks of differing characteristics. As such, the MPET equations represent a generalization of Biot’s equations, and numerical discretizations of the MPET equations face similar challenges. Here, we focus on the nearly incompressible case for which standard mixed finite element discretizations of the MPET equations perform poorly. Instead, we propose a new mixed finite element formulation based on introducing an additional total pressure variable. By presenting energy estimates for the continuous solutions and a priori error estimates for a family of compatible semi-discretizations, we show that this formulation is robust in the limits of incompressibility, vanishing storage coefficients, and vanishing transfer between networks. These theoretical results are corroborated by numerical experiments. Our primary interest in the MPET equations stems from the use of these equations in modelling interactions between biological fluids and tissues in physiological settings. So, we additionally present physiologically realistic numerical results for blood and tissue fluid flow interactions in the human brain.

New preprint on multilevel Monte Carlo with non-nested meshes available!

Our new paper on Efficient white noise sampling and coupling for multilevel Monte Carlo with non-nested meshes is now available on arXiv!


When solving stochastic partial differential equations (SPDEs) driven by additive spatial white noise, the efficient sampling of white noise realizations can be challenging. In this paper, we present a new sampling technique that can be used to efficiently compute white noise samples in a finite element method and multilevel Monte Carlo (MLMC) setting. The key idea is to exploit the finite element matrix assembly procedure and factorize each local mass matrix independently, hence avoiding the factorization of a large matrix. Moreover, in a MLMC framework, the white noise samples must be coupled between subsequent levels. We show how our technique can be used to enforce this coupling even in the case of non-nested mesh hierarchies. We demonstrate the efficacy of our method with numerical experiments. We observe optimal convergence rates for the finite element solution of the elliptic SPDEs of interest in 2D and 3D and we show convergence of the sampled field covariances. In a MLMC setting, a good coupling is enforced and the telescoping sum is respected.

New preprint investigating the effects of uncertainty on cardiac mechanics


Our new paper on Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response is now available on arxiv!

Computational cardiac modelling is currently evolving from a pure research tool to aiding in clinical decision making. Assessing the reliability of computational model predictions is a key factor for clinical use, and uncertainty quantification (UQ) and sensitivity analysis are important parts of such an assessment. In this study, we apply new methods for UQ in computational heart mechanics to study uncertainty both in material parameters characterizing global myocardial stiffness and in the local muscle fiber orientation that governs tissue anisotropy. The uncertainty analysis is performed using the polynomial chaos expansion (PCE) method, which is a non-intrusive meta-modeling technique that surrogates the original computational model with a series of orthonormal polynomials over the random input parameter space. In addition, in order to study variability in the muscle fiber architecture, we model the uncertainty in orientation of the fiber field as an approximated random field using a truncated Karhunen-Loéve expansion. The results from the UQ and sensitivity analysis identify clear differences in the impact of various material parameters on global output quantities. Furthermore, our analysis of random field variations in the fiber architecture demonstrate a substantial impact of fiber angle variations on the selected outputs, highlighting the need for accurate assignment of fiber orientation in computational heart mechanics models.

New paper investigating the effect of injection parameters on drug delivery in the spinal canal published!

pizzichelliOur paper titled Numerical study of intrathecal drug delivery to a permeable spinal cord: effect of catheter position and angle is now published. Intrathecal delivery is a procedure involving the release of therapeutic agents into the cerebrospinal fluid (CSF) through a catheter. It holds promise for treating high-impact central nervous system pathologies, for which systemic administration routes are ineffective. In this study we introduce a numerical model able to simultaneously account for solute transport in the fluid and in the spinal cord. Using a Discontinuous Galerkin method and a three-dimensional patient-specific geometry, we studied the effect of catheter position and angle on local spinal cord drug concentration. Based on our simulations, lateral injection perpendicular to the cord turned out to be more effective than other configurations.

New paper on new numerics for an emerging modelling framework for biological cells published!

figure1Our paper on A Cell-Based Framework for Numerical Modeling of Electrical Conduction in Cardiac Tissue is now (open access) published! In this paper, we study a mathematical model of cardiac tissue based on explicit representation of individual cells. In this EMI model, the extracellular (E) space, the cell membrane (M), and the intracellular (I) space are represented as separate geometrical domains. This representation introduces modeling flexibility needed for detailed representation of the properties of cardiac cells including their membrane. In particular, we will show that the model allows ion channels to be non-uniformly distributed along the membrane of the cell. Such features are difficult to include in classical homogenized models like the monodomain and bidomain models frequently used in computational analyses of cardiac electrophysiology.

New paper on high resolution data assimilation for cardiac mechanics published

outputOur paper on High-resolution data assimilation of cardiac mechanics applied to a dyssynchronous ventricle is now published! Computational models of cardiac mechanics, personalized to a patient, offer access to mechanical information above and beyond direct medical imaging. Additionally, such models can be used to optimize and plan therapies in-silico, thereby reducing risks and improving patient outcome. Model personalization has traditionally been achieved by data assimilation, which is the tuning or optimization of model parameters to match patient observations. Current data assimilation procedures for cardiac mechanics are limited in their ability to efficiently handle high-dimensional parameters. This restricts parameter spatial resolution, and thereby the ability of a personalized model to account for heterogeneities that are often present in a diseased or injured heart. In this paper, we address this limitation by proposing an adjoint gradient–based data assimilation method that can efficiently handle high-dimensional parameters. We test this procedure on a synthetic data set and provide a clinical example with a dyssynchronous left ventricle with highly irregular motion. Our results show that the method efficiently handles a high-dimensional optimization parameter and produces an excellent agreement for personalized models to both synthetic and clinical data.


New paper on estimating cardiac activation from surface measurements published

Our paper on Inverse estimation of cardiac activation times via gradient-based optimisation is now published online in the International Journal for Numerical Methods in Biomedical Engineering! In this study, we use a PDE-constrained optimal control approach to numerically investigate the identifiability of an initial activation sequence from synthetic observations of the extracellular potential using the bidomain approximation and 2D representations of heart tissue. Our results demonstrate that activation times and duration of several stimuli can be recovered even with high levels of noise, that it is sufficient to sample the observations at the ECG-relevant sampling frequency of 1 kHz, and that spatial resolutions that are coarser than the standard in electrophysiological simulations can be used.graphical_abstract