Three-dimensional simulation of unstable gravity-driven infiltration of water into a porous medium

Infiltration of water in dry porous media is subject to a powerful gravity-driven instability. Although the phenomenon of unstable infiltration is well known, its description using continuum mathematical models has posed a significant challenge for several decades. The classical model of water flow in the unsaturated flow, the Richards equation, is unable to reproduce the instability. Here, we present a computational study of a model of unsaturated flow in porous media that extends the Richards equation and is capable of predicting the instability and captures the key features of gravity fingering quantitatively. The extended model is based on a phase-field formulation and is fourth-order in space. The new model poses a set of challenges for numerical discretizations, such as resolution of evolving interfaces, stiffness in space and time, treatment of singularly perturbed equations, and discretization of higher-order spatial partial–differential operators. We develop a numerical algorithm based on Isogeometric Analysis, a generalization of the finite element method that permits the use of globally-smooth basis functions, leading to a simple and efficient discretization of higher-order spatial operators in variational form. We illustrate the accuracy, efficiency and robustness of our method with several examples in two and three dimensions in both homogeneous and strongly heterogeneous media. We simulate, for the first time, unstable gravity-driven infiltration in three dimensions, and confirm that the new theory reproduces the fundamental features of water infiltration into a porous medium. Our results are consistent with classical experimental observations that demonstrate a transition from stable to unstable fronts depending on the infiltration flux.United States. Dept. of Energy (Early Career Award Grant DE-SC0003907

Computer simulation of glioma growth and morphology

Despite major advances in the study of glioma, the quantitative links between intra-tumor molecular/cellular properties, clinically observable properties such as morphology, and critical tumor behaviors such as growth and invasiveness remain unclear, hampering more effective coupling of tumor physical characteristics with implications for prognosis and therapy. Although molecular biology, histopathology, and radiological imaging are employed in this endeavor, studies are severely challenged by the multitude of different physical scales involved in tumor growth, i.e., from molecular nanoscale to cell microscale and finally to tissue centimeter scale. Consequently, it is often difficult to determine the underlying dynamics across dimensions. New techniques are needed to tackle these issues. Here, we address this multi-scalar problem by employing a novel predictive three-dimensional mathematical and computational model based on first-principle equations (conservation laws of physics) that describe mathematically the diffusion of cell substrates and other processes determining tumor mass growth and invasion. The model uses conserved variables to represent known determinants of glioma behavior, e.g., cell density and oxygen concentration, as well as biological functional relationships and parameters linking phenomena at different scales whose specific forms and values are hypothesized and calculated based on in vitro and in vivo experiments and from histopathology of tissue specimens from human gliomas. This model enables correlation of glioma morphology to tumor growth by quantifying interdependence of tumor mass on the microenvironment (e.g., hypoxia, tissue disruption) and on the cellular phenotypes (e.g., mitosis and apoptosis rates, cell adhesion strength). Once functional relationships between variables and associated parameter values have been informed, e.g., from histopathology or intra-operative analysis, this model can be used for disease diagnosis/prognosis, hypothesis testing, and to guide surgery and therapy. In particular, this tool identifies and quantifies the effects of vascularization and other cell-scale glioma morphological characteristics as predictors of tumor-scale growth and invasion

Lattice and Continuum Modelling of a Bioactive Porous Tissue Scaffold

A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for tissue engineering applications make use of spatially homogeneous or spatially continuous equations to model cell growth, flow of culture medium, nutrient transport, and their interactions. The network structure of the physical porous scaffold is often incorporated through parameters in these models, either phenomenologically or through techniques like mathematical homogenization. We derive a model on a square grid lattice to demonstrate the importance of explicitly modelling the network structure of the porous scaffold, and compare results from this model with those from a modified continuum model from the literature. We capture two-way coupling between cell growth and fluid flow by allowing cells to block pores, and by allowing the shear stress of the fluid to affect cell growth and death. We explore a range of parameters for both models, and demonstrate quantitative and qualitative differences between predictions from each of these approaches, including spatial pattern formation and local oscillations in cell density present only in the lattice model. These differences suggest that for some parameter regimes, corresponding to specific cell types and scaffold geometries, the lattice model gives qualitatively different model predictions than typical continuum models. Our results inform model selection for bioactive porous tissue scaffolds, aiding in the development of successful tissue engineering experiments and eventually clinically successful technologies.Comment: 38 pages, 16 figures. This version includes a much-expanded introduction, and a new section on nonlinear diffusion in addition to polish throughou

Computational phase-field modeling

Phase-field modeling is emerging as a promising tool for the treatment of problems with interfaces. The classical description of interface problems requires the numerical solution of partial differential equations on moving domains in which the domain motions are also unknowns. The computational treatment of these problems requires moving meshes and is very difficult when the moving domains undergo topological changes. Phase-field modeling may be understood as a methodology to reformulate interface problems as equations posed on fixed domains. In some cases, the phase-field model may be shown to converge to the moving-boundary problem as a regularization parameter tends to zero, which shows the mathematical soundness of the approach. However, this is only part of the story because phase-field models do not need to have a moving-boundary problem associated and can be rigorously derived from classical thermomechanics. In this context, the distinguishing feature is that constitutive models depend on the variational derivative of the free energy. In all, phase-field models open the opportunity for the efficient treatment of outstanding problems in computational mechanics, such as, the interaction of a large number of cracks in three dimensions, cavitation, film and nucleate boiling, tumor growth or fully three-dimensional air-water flows with surface tension. In addition, phase-field models bring a new set of challenges for numerical discretization that will excite the computational mechanics community

Reactive Flows in Deformable, Complex Media

Many processes of highest actuality in the real life are described through systems of equations posed in complex domains. Of particular interest is the situation when the domain is variable, undergoing deformations that depend on the unknown quantities of the model. Such kind of problems are encountered as mathematical models in the subsurface, or biological systems. Such models include various processes at different scales, and the key issue is to integrate the domain deformation in the multi-scale context. Having this as the background theme, this workshop focused on novel techniques and ideas in the analysis, the numerical discretization and the upscaling of such problems, as well as on applications of major societal relevance today