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Discretization of flow in fractured porous media commonly lead to large systems of linear equations that require dedicated solvers. In this work, we develop an efficient linear solver and its practical implementation for mixed-dimensional…
Intelligent biological systems are characterized by their embodiment in a complex environment and the intimate interplay between their nervous systems and the nonlinear mechanical properties of their bodies. This coordination, in which the…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences.…
In this paper, we present a computational framework based on fully Eulerian models for fluid-structure interaction for the numerical simulation of biological capsules. The flexibility of such models, given by the Eulerian treatment of the…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
In this paper, we propose a parallel solver for solving the quasi-static linear poroelasticity coupled with linear elasticity model in the Lagrange multiplier framework. Firstly, we reformulate the model into a coupling of the nearly…
Precipitation of fine particles into the base material of a metal is a potent strengthening mechanism. This is numerically analyzed within a continuum framework based on a higher order strain gradient plasticity theory and by use of an…
Detailed understanding of the coupling between fluid flow and solid deformation in porous media is crucial for the development biomedical devices and novel energy technologies relating to a wide range of geological and biological processes.…
Porous media processes involve various physical phenomena such as mechanical deformation, transport, and fluid flow. Accurate simulations must capture the strong couplings between these phenomena. Choosing an efficient solver for the…
In this paper we propose a variant of the substructuring preconditioner for solving three-dimensional elliptic-type equations with strongly discontinuous coefficients. In the proposed preconditioner, we use the simplest coarse solver…
Cross-sections of cell shapes in a tissue monolayer typically resemble a tiling of convex polygons. Yet, examples exist where the polygons are not convex with curved cell-cell interfaces, as seen in the adaxial epidermis. To date,…
Unfitted finite element methods, e.g., extended finite element techniques or the so-called finite cell method, have a great potential for large scale simulations, since they avoid the generation of body-fitted meshes and the use of graph…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
We aim to solve the incompressible Navier-Stokes equations within the complex microstructure of a porous material. Discretizing the equations on a fine grid using a staggered (e.g., marker-and-cell, mixed FEM) scheme results in a nonlinear…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Despite the ubiquity of fluid flows interacting with porous and elastic materials, we lack a validated non-empirical macroscale method for characterizing the flow over and through a poroelastic medium. We propose a computational tool to…
Computational simulations have the potential to assist in liver resection surgeries by facilitating surgical planning, optimizing resection strategies, and predicting postoperative outcomes. The modeling of liver tissue across multiple…
Numerical simulation of fracture contact poromechanics is essential for various applications, including CO2 sequestration, geothermal energy production and underground gas storage. Modeling this problem accurately presents significant…
Magnetic Resonance Elastography allows noninvasive visualization of tissue mechanical properties by measuring the displacements resulting from applied stresses, and fitting a mechanical model. Poroelasticity naturally lends itself to…