Related papers: Analysis of the spatial and dynamical properties o…
The cellular Potts model (CPM) is a powerful computational method for simulating collective spatiotemporal dynamics of biological cells. To drive the dynamics, CPMs rely on physics-inspired Hamiltonians. However, as first principles remain…
We present a mechanical model of tissue homeostasis that is specialised to the intestinal crypt. Growth and deformation of the crypt, idealised as a line of cells on a substrate, are modelled using morphoelastic rod theory. Alternating…
Colorectal cancers are the third most common type of cancer. They originate from intestinal crypts, glands that descend from the intestinal lumen into the underlying connective tissue. Normal crypts are thought to exist in a dynamic…
The self renewal process in colonic crypts is the object of several studies. We present here a new compartment model with the following characteristics: a) We distinguish different classes of cells: stem cells, 6 generations of transit…
In this work, we study a system of degenerate parabolic equations modeling the dynamics of multiple cell populations in intestinal crypts. The model describes cell division, differentiation, and migration through a strongly coupled system…
Intestinal enteroendocrine cells secrete hormones that are vital for the regulation of glucose metabolism but their differentiation from intestinal stem cells is not fully understood. Asymmetric stem cell divisions have been linked to…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Cellular Potts models are broadly applied across developmental biology and cancer research. We overcome limitations of the traditional approach, which reinterprets a modified Metropolis sampling as ad hoc dynamics, by introducing a physical…
We present a development of a model of the relationship between cells in three compartments of the intestinal crypt: stem cells, semi-differentiated cells and fully differentiated cells. Stem and semi-differentiated cells may divide to…
Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…
The Spatial Processes package enables an explicit definition of a spatial environment on top of the normal dynamic modeling SBML capabilities. The possibility of an explicit representation of spatial dynamics increases the representation…
Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This…
In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes…
The Cellular Potts Model (CPM) succesfully simulates drainage and shear in foams. Here we use the CPM to investigate instabilities due to the flow of a single large bubble in a dry, monodisperse two-dimensional flowing foam. As in…
The advantage of Cellular Potts Model (CPM) is due to its ability for introducing cell-cell interaction based on the well known statistical model i.e. the Potts model. On the other hand, Lattice gas Cellular Automata (LGCA) can simulate…
The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in…
We investigate some chemostat models incorporating wall growth, competition, random fluctuations on the dilution rate, and different consumption functions (Monod and Haldane). We analyze the asymptotic behavior of the solutions of the…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…
The neural dynamics of the nematode C. elegans are experimentally low-dimensional and correspond to discrete behavioral states, where previous modeling work has found neural proxies for some of these states. Experimental results further…