elifesciences-publications / 3dhypocotyl Goto Github PK

The files provided via this project are used to run mechanical growth simulations of 3D hypocotyls using the Tissue simulation software, and can be used to produce the computational model output in Bou Daher et al (2018). The simulations include cell wall mechanics where individual walls can have specified (asymmetric or anisotropic) elastisities; pressure and anisotropic forces can be applied, and growth is modelled using a Lockhart type of growth rule.

Bou Daher F, Chen Y, Bozorg B, Heywood Clough J, Jönsson H, Braybrook SA (2018) Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry eLife ( and bioRxiv).

We have divided the files into two directories, each containing the files needed to generate the results presented in Fig4 and FigS4, respectively. In the directories files of the types described below can be found.

• README.txt files contain instructions on how to run simulations to generate the individual results.

• *.model files contain all the parameter values for the mechanical and growth rules.

• *.init files contain the initial geometry description, including flags for defining different type of walls to be given special mechanical properties.

• *.rk files contain instructions to the solver on e.g. time of simulation and output format.

• hypocotyl3D.pvsm files has information for 3D visualisation of the output structure in Paraview (see Output section below).

• *.data files hold data, such as length, for plotting different graphs.

All simulations have been performed using the in-house developed c++ solver Tissue. Installation and compiling instructions can be found via the wiki page.

In short, a simulation is run by providing a set of .model, .init, and .rk files at terminal:

TISSUE/bin/solver example.model example.init example.rk

where TISSUE is the full path to the directory where tissue was downloaded and it is assumed you are in the directory where the model/init/rk files are stored. This will generate a vtk directory where output files are stored. A descrption on what the individual reations/rules defined in the *.model file does is provided in the Tissue Documentation. This is also true for the format of the *.init and *.rk files.

Hypocotyl geometries are stored as vtk files (in the vtk directory) during the simulation and the user can specify how often a 'snapshot' should be taken (in the *.rk files). These can for example be visualised using Paraview (see example Figure) Settings for the visualisations are found in the files *.pvsm that can be loaded into paraview by File/Load State... followed by selecting the vtk directory of the output.

Behruz Bozorg ([email protected])
Henrik Jönsson ([email protected])
Siobhan Braybrook ([email protected])