In this paper we present a critical comparison of the suitability of several numerical methods, level set, moving grid and phase field model, to address two well known Stefan problems in phase transformation studies: melting of a pure phase and diffusional solid state phase transformations in a binary system. Similarity solutions are applied to verify the numerical results. The comparison shows that the type of phase transformation considered determines the convenience of the numerical techniques. Finally, it is shown both numerically and analytically that the solid-solid phase transformation is a limiting case of the solid-liquid transformation.

We consider the movement and viability of individual cells in cell colonies. Cell movement is assumed to take place as a result of sensing the strain energy density as a mechanical stimulus. The model is based on tracking the displacement and viability of each individual cell in a cell colony. Several applications are shown, such as the dynamics of filling a gap within a fibroblast colony and the invasion of a cell colony. Though based on simple principles, the model is qualitatively validated by experiments on living fibroblasts on a flat substrate.

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Biogrout is a new soil reinforcement method based on microbial-induced carbonate precipitation. Bacteria are placed and reactants are flushed through the soil, resulting in calcium carbonate precipitation, causing an increase in strength and stiffness of the soil. Due to this precipitation, the porosity of the soil decreases. The decreasing porosity influences the permeability and therefore the flow. To analyse the Biogrout process, a model was created that describes the process. The model contains the concentrations of the dissolved species that are present in the biochemical reaction. These concentrations can be solved from a advection-dispersion-reaction equation with a variable porosity. Other model equations involve the bacteria, the solid calcium carbonate concentration, the (decreasing) porosity, the flow and the density of the fluid. The density of the fluid changes due to the biochemical reactions, which results in density driven flow. The partial differential equations are solved by the Standard Galerkin finite-element method. Simulations are done for some 1D and 2D configurations. A 1D configuration can be used to model a column experiment and a 2D configuration may correspond to a sheet or a cross section of a 3D configuration.Keywords Biogrout · Microbial-induced carbonate precipitation · Density flow · Finite-element method · Decreasing porosity List of Symbols

Dissolution of stoichiometric multi-component particles is an important process occurring during the heat treatment of as-cast aluminum alloys prior to hot extmsion. A mathematical model is proposed to describe such a process. In this model equations are given to determine the position of the particle interface in time, using a number of diffusion equations which are coupled by nonlinear boundary conditions at the interface. This problem is known as a vector valued Stefan problem. A necessary condition for existence of a solution of the moving boundary problem is proposed and investigated using the maximum principle for the parabolic paiiial differential equation. Furthermore, for an unbounded domain and planar co-ordinates an asymptotic approximation based on self-similarity is derived. The asymptotic approximation is used to gain insight into the influence of all components on the dissolution. Subsequently, a numerical treatment of the vector valued Stefan problem is described. The numerical solution is compared with solutions obtained by the analytical methods.Finally, an example is shown.

Cell migration plays an essential role in cancer metastasis. In cancer invasion through confined spaces, cells must undergo extensive deformation, which is a capability related to their metastatic potentials. Here, we simulate the deformation of the cell and nucleus during invasion through a dense, physiological microenvironment by developing a phenomenological computational model. In our work, cells are attracted by a generic emitting source (e.g., a chemokine or stiffness signal), which is treated by using Green’s Fundamental solutions. We use an IMEX integration method where the linear parts and the nonlinear parts are treated by using an Euler backward scheme and an Euler forward method, respectively. We develop the numerical model for an obstacle-induced deformation in 2D or/and 3D. Considering the uncertainty in cell mobility, stochastic processes are incorporated and uncertainties in the input variables are evaluated using Monte Carlo simulations. This quantitative study aims at estimating the likelihood for invasion and the length of the time interval in which the cell invades the tissue through an obstacle. Subsequently, the two-dimensional cell deformation model is applied to simplified cancer metastasis processes to serve as a model for in vivo or in vitro biomedical experiments.Electronic supplementary materialThe online version of this article (10.1007/s10237-018-1036-5) contains supplementary material, which is available to authorized users.

A continuum hypothesis-based model is developed for the simulation of the (long term) contraction of skin grafts that cover excised burns in order to obtain suggestions regarding the ideal length of splinting therapy and when to start with this therapy such that the therapy is effective optimally. Tissue is modeled as an isotropic, heterogeneous, morphoelastic solid. With respect to the constituents of the tissue, we selected the following constituents as primary model components: fibroblasts, myofibroblasts, collagen molecules, and a generic signaling molecule. Good agreement is demonstrated with respect to the evolution over time of the surface area of unmeshed skin grafts that cover excised burns between outcomes of computer simulations obtained in this study and scar assessment data gathered previously in a clinical study. Based on the simulation results, we suggest that the optimal point in time to start with splinting therapy is directly after placement of the skin graft on its recipient bed. Furthermore, we suggest that it is desirable to continue with splinting therapy until the concentration of the signaling molecules in the grafted area has become negligible such that the formation of contractures can be prevented. We conclude this study with a presentation of some alternative ideas on how to diminish the degree of contracture formation that are not based on a mechanical intervention, and a discussion about how the presented model can be adjusted.