MorphoDynamX

The next generation of the MorphoGraphX software

A tool for computational Morphodynamics

with two powerful AddOns included:

What is MorphoDynamX?

MorphoDynamX is based on a data structure called Cell Complexes that are ideal for modeling subdividing geometry in 2 and 3 dimensions. MorphoDynamX integrated image processing with simulation modeling, and allows models to run directly on templates extracted from imaging data.

Simulation of Phyllotaxis on a shoot apex using a Meinhardt activator-inhibitor system. The simulation combines a molecular network, cell-cell signaling, growth, and cell division. As the apex grows, space opens up at the tip for a new leaf to form. Green represents the concentration of the activator.

MorphoMechanX


MorphoMechanX is an AddOn for MorphoDynamX that enables the mechanical modeling of biological tissues by means of Finite Element Method (FEM) for solid mechanics. Unlike engineering FEM softwares, MorphoMechanX is specialized for elements that grow and subdivide, and allows growth and mechanics to interact with genetic network simulation in MorphoDynamX. The software is highly parallelized by means of the Thrust library which can use Cuda on nVidia GPUs or OMP on the host processor.

MorphoMechanX is developed in collaboration with Gabriella Mosca, and has evolved from her PhD work.

Steady state mechanics

Simulation showing the turgor induced stresses on a template extracted from confocal images of Arabidopsis puzzle cells (see Sapala et al. 2018, eLife).

Realistic templates extracted with MorphoGraphX, or idealized plant cells are inflated with turgor pressure and the resulting stresses visualized. These simulations are primarily used to study the effect of cell geometry on stress, or to interpret the results of micro-indentation experiments performed with the Cellular Force Microscope (CFM) and its controlling software MorphoRobotX.

Dynamic growth mechanics

Simulation of growth on a continuous tissue. Increased growth of the top causes the structure to buckle like a daffodil corona.

MorphoMechanX allows finite elements to grow, with growth specified directly as model parameters, or from the output of molecular signaling networks performed in MorphoDynamX. The software can be used both for cellular models and continuous tissue simulation.

MorphoRobotX


MorphoRobotX is an AddOn to MorphoDynamX that is used to control the Cellular Force Microscope, a custom microindentation system that is specialized for plants. MorphoRobotX uses the visualization framework for MorphoDynamX, and allows the visualization of both confocal images and indentation experiments together.

Surface scan of an onion epidermal peel, colored by height.

MorphoDynamX will be available for public release soon

To obtain a pre-release copy of MorphoMechanX and sample models, please email Richard Smith

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