This repo contains simulation and data analysis methods of the research article titled "Multi-condensate state as a functional strategy to optimize the cell signaling output".
- Figure 1 contains files related to Langevin Dynamics simulations, using the LAMMPS software. Instructions on how to run lammps
- Figure 2 and Figure 3 contains files related to reaction-diffusion simulations using the Virtual Cell software
- Figure 4 contains python files related to the analytical solutions of the Ordinary Differential Equation (ODE)
- Figure 5 contains python files to solve ODEs with a distribution of cluster sizes
- Supplementary_data contains Virtaul Cell input files as well as the source data visualized in Figures 1, 2 and 3.
Requirements: (Versions of the softwares used in this study are listed here)
- LAMMPS executable: lammps-5Jun19
- Simulations are run on Harvard FAS RC. As of 05/13/2024, modules: gcc/13.2.0-fasrc01, openmpi/4.1.5-fasrc03
- Virtual Cell: VCell 7.5.0 (build 62)
- Python:
- conda version: 23.3.1
- conda-build version : 3.23.3
- python version : 3.10.9
- platform : win-64
- user-agent : conda/23.3.1 requests/2.28.1 CPython/3.10.9 Windows/10
- Numpy version: 1.24.3
- Matplotlib version: 3.7.0
- Pandas version: 1.5.3
- Nrrrd module: 1.0.0