Published Models

This multiscale mechanistic liver lobule model is composed of various interacting cell types, such as hepatocytes, residential Kupffer cells and macrophages. It captures hepatocellular acetaminophen (APAP) metabolism, DNA damage response activation, necrotic cell death, macrophage recruitment and the regulation of hepatocellular senescence and proliferation, with qualitatively different outcomes as a function of the initial APAP concentration in blood plasma.

Introduction Comparison of spatio-temporal model output to experimental measurements or between model variants all require the application of summary statistics. For multicellular models, statistical properties of the cell configuration at given times or across time are of interest and Morpheus provides some Analysis/Trackers for that: CellTracker, DisplacementTracker, ClusteringTracker and ContactLogger.

Different cell migration patterns may result from different dynamic states like wave pinning (WP), mixed-mode oscillations (MMO) and relaxation oscillations (RO) of the Rho-Rac-paxillin circuit on the cell membrane.

The migration of zebrafish polster cells is oriented by the migration of follower cells, allowing robust long-range coordination of different cell populations. Introduction Collective cell migration is an important process during biological development and tissue repair.

Guidance-by-followers combined with one of several simple rule sets for integration of signals from multiple neighbors provides a robust mechanism for collective cell migration. Introduction Collective cell migration is an important process during biological development and tissue repair but may turn malignant during tumor invasion.

Introduction Larvae of the nematode Caenorhabditis elegans aggregate into clusters of several hundred moving individuals when starved during their first larval stage (see video below). Avery et al. proposed that starved larvae produce and respond chemotactically to two diffusible chemical signals, a short-range attractant and a longer range repellent.

Introduction Collective motion of human breast cancer cells of the cell line MDA-MB-231 was studied by Lee et al. for individual crawling cells, cell doublets, cell quadruplets and for confluent populations on a two-dimensional substrate.

Introduction Brook et al. studied the effect of distinct immune phenotypes on cellular-scale viral propagation in three mammalian kidney cell lines with different interferon pathways (IFN). Differences in the IFN response upon pathogen invasion allowed to experimentally observe, model and numerically simulate viral dynamics in cells with

Introduction In Jagiella et al. 2017 a quantitative single cell-based mathematical model for multi-cellular tumor spheroids was parametrized by Bayesian inference for different scenarios of nutrition and oxygen supply. The simulations generate of the order of a million individual cells.

Multiscale simulation of EMT by minimal signaling circuit Introduction We model epithelial-mesenchymal transition (EMT) by first assembling an ODE model for intracellular Yes-associated protein (YAP) signalling and then embedding this single cell model within individual cells in a multiscale simulation.