L. Brusch

Introduction Human induced pluripotent stem cells (hiPSCs) can be grown in cell culture where they self-organize spatial patterns. Libby et al. have employed inducible CRISPR interference-driven genetic perturbations to modulate mechanical cell properties like cell-cell adhesion and cortical tension.

Introduction The formation and maintenance of three germ layers in colonies of human embryonic stem cells (ESCs) is sensitive to the geometry of the colony. In vitro experiments with micropatterns controlling colony shape have previously addressed the underlying spatio-temporal patterning in Warmflash et al.

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

This example model demonstrates how to obtain consistent results in physical units together with the freedom to choose arbitrary lattice and time discretizations. Introduction Often, one starts to build a model with a particular lattice size and time scaling.

Pattern formation is robust to noise. Introduction Morpheus can also simulate ODE and PDE models with noise. One example (in the GUI menu Examples → ODE → LateralSignaling.xml) with coupled noisy ODE systems is explained in M0004.

Diffusion in Liver Lobule Introduction This model considers diffusion of a marker with concentration $c(x,y,t)$ across a liver lobule. The lobule is patterned into a central zone around the central vein (center of simulation domain) and portal zones around (here six) portal triads that here act as sinks ($c = 0$).

Introduction The mass-conserving secretion and uptake of (signaling) molecules by cells can in Morpheus be achieved with Mappers and scaling fluxes by cell.volume. The intracellular amount of signal may trigger a change in a state variable that could downstream change cell behaviors.

Track MotherId (cell.id of mother) and compare it between neighboring cells Introduction This example model demonstrates the tracking of the cell.id of any cell’s mother and to compare these MotherIds between neighboring cells upon contact to trigger special behaviors if sister cells meet in a SisterReunion.

Use logical operators and, or and xor in Condition for ChangeCellType. Introduction This example model demonstrates the use of logical operators. Please also see the built-in docu at GUI/Documentation/MathematicalExpressions.