A simple biophysical model for chromosome condensation simulations
‘Chromosome-condesation’ code is a C++ biophysical software designed for Brownian dynamics of chromatin condensation with two distinct mechanisms – ‘diffusion capture’ which is based on pairwise interactions between chromatin loci or between particles mimicking condensin/cohesin, and ‘loop extrusion’, resulting in formation of chromatin loops. ‘Chromo-sim’ can be also used for simple Brownian dynamics simulations of free polymers without any condensation mechanisms (Yasu’s paper). For in-depth description of the model and biophysical algorithms applied, please see https://www.biorxiv.org/content/10.1101/2020.10.15.341305v1.
This is an example of how you may set up the code running for your projects locally.
- C++ built-in
- Visualization software such as Chimera, VMD or PyMOL
- You can download the code (
initConfig.hpp, initConfig.cpp, initDynamics.hpp, initDynamics.cpp, chromoCell.cpp, Makefile) - Or you can clone the repo: git clone https://github.com/FrancisCrickInstitute/Chromosome-Condensation
First, create a folder where you want to run simulations:
mkdir test_sim
cd test_sim
Make sure you copy all the code files from chromo_sim_code to the folder where you want to run simulations:
cp path_to_code_folder/chromo_sim_code/* ./
Next, set up parameters in the initConfig.hpp (for parameter description see Documentation) and then compile the code:
make
Run the simulation:
./chromo
The main output of code are PDB files from specific timepoints with coordinates of polymer and condensin/cohesin proteins. These can be visalized using Chimera, VMD or PyMOL. There are additional output files to monitor further events in the simulations (Documentation) you can opt for.
The ‘Chromosome-condensation’ code consists of several files:
- initConfig.hpp = includes parameter settings and declaration of functions that initialise the chromatin chain and binders
- initConfig.cpp = includes definition of functions that initialise the chromatin chain and binders
- initDynamics.hpp = includes declaration of functions that describe the dynamical evolution of chromatin chain and binders, including those detail rules of diffusion capture and loop extrusion
- initDynamics.cpp = includes definition of functions that describe the dynamical evolution of chromatin chain and binders, including those detail rules of diffusion capture and loop extrusion
- chromoCell.cpp = includes functions to call functions in files above to simulate the dynamical evolution of chromatin condensation
General parameter set up can be adjusted in initConfig.hpp file. README_parameters.xlsx contains more in-depth description of polymer simulation parameters.
Optional output files and their corresponding parameters are: • chromoPDB*.pdb = PDB file format of chromatin chain with binders/condensin in selected time point
• DC_stats_index2.txt = number of diffusion capture interactions/pairs in time
• binder_attach_site.txt = site on chromatin chain where binders are attached
• loop_size.txt = loops sizes in time
• nested_loops.txt = number of nested loops in time
• voxMap_occupancy.txt = number of beads in each voxel
• voxMap_occupancy2new.txt = number of occupied voxels
• msd_bead_coord.txt = coordinate monitoring in selected time windows, used for further MSD and anisotropy calculations
Distributed under The Francis Crick Institute License.
- Tereza Gerguri - @GerguriTereza, tereza.gerguri@crick.ac.uk
- Xiao Fu - @foolbirdie, xiao.fu@crick.ac.uk
- Paul Bates - @PaulBatesBMM, paul.bates@crick.ac.uk
This code was developed under the Biomolecular Modelling Laboratory https://www.crick.ac.uk/research/labs/paul-bates at Francis Crick Institute (https://www.crick.ac.uk/ ) as a part of collaboration with Chromosome Segregation Laboratory https://www.crick.ac.uk/research/labs/frank-uhlmann. Please cite our paper (https://www.biorxiv.org/content/10.1101/2020.10.15.341305v1) when using the code.