Simulations of nuclear droplets diffusion + fusion.
3D agent-based simulations implemented in C++ used in our paper [Al Jord et al., bioRxiv] to simulate diffusion of nuclear speckles with possibility of fusion upon contact. Obstacles can be added to mimick nuclear confinement and can be condensed around the nucleolus to reproduce DNA condensation in NSN to SN transition in mouse oocytes.
The template configuration files to reproduce the simulations presented in our paper are available in the parameters folder.
Esfera is a C++ software that can be runned through the command line. A Makefile is available in this repository to compile it and it can be runned with the corresponding configuration file (an xml file) that contains the parameters of the simulation. The output files (txt files) containing the position of each sphere at the output times are created in a output folder in the folder where the simulation is runned.
To visualize the output of the simulations, we used Paraview. Paraview configuration files that allow to display directly the output files are given in this repository in the folder paraviewfiles.
Cytoplasmic forces functionally reorganize nuclear condensates in oocytes
Adel Al Jord, Gaelle Letort, Adrien Eichmuller, Soline Chanet, Jean-René Huynh, Nir S. Gov, Raphael Voituriez, Marie-Emilie Terret, Marie-Helene Verlhac
bioRxiv doi:10.1101/2021.03.15.434387
If you use this code or an adaptation of it, please cite our paper, or use this DOI:
This code was developped in the Terret/Verlhac team at the Centre de Recherche Interdisciplinaire en Biologie in the College de France.
Esfera is freely available open-source under the GNU GPL v3.0 License (see License file).