https://github.com/cycelslab/latticemtcrowdantsim
Simulating the effect of crowdant size and concentration on collective microtubule polymerization dynamics using a square lattice based simulation
Science Score: 26.0%
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Low similarity (9.3%) to scientific vocabulary
Repository
Simulating the effect of crowdant size and concentration on collective microtubule polymerization dynamics using a square lattice based simulation
Basic Info
- Host: GitHub
- Owner: CyCelsLab
- Language: C++
- Default Branch: main
- Size: 37.1 KB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
randomWalkWithCrowdants
This simulates a square lattice based diffusion and crowdant dynamics involved in linear polymer elongation.
Instructions on running the code (for MAC OSX 13.5.2 (22G91) Ventura) on Terminal with MacPorts for Linux compatability)
1. Download code into a folder and unzip
2. Ensure /yaml-cpp is downloaded and compiled (ref. makefile option >>make install)
3. In the directory /randomWalkWithCrowdants/ run >>make done
4. A directory ./bin should be estabilished if the code compiled with the file ./bin/mmc
5. Run the code using the command >>./bin/mmc [folder name]
[folder name] directory will be made under directory Data where all data files will be saved.
6. Outputs should be in the form
time 99830 time 99840 time 99850 time 99860 time 99870 time 99880 time 99890 time 99900 time 99910 7. Visualizing the output requires depending on the task: >>python movie-diff.py _>>python reading-log-file.py [Data/folder name] 8. For polymerisation stats, a python script reading-log-file.py can be used in a following manner. python3 reading-log-file.py [Data/folder name] where [Data/folder name] points to the folder within the code directory where the outputs from the current run are stored. 9. 2D lattice time-series can be visualised frame by frame with .PNG images generated by using the command: _>>python3 movie-diff.py Note: movie-diff.py needs some manual interventions such as size of the lattice, size of the monomer and crowdants. This can be done interactively by editing the file. 10. For visualising the polymer number dynamics, number of polymer of suze "i" with time _>> python3 reading-pol-file.py [Data/folder name] 11. For plotting the probability distribution of the polymer length distribution at any saved iteration _>> python3 hist-plot.py [Data/folder name] [i] # comment note: i is the integer
Owner
- Name: Cytoskeleton and Cell Shape (CyCelS)
- Login: CyCelsLab
- Kind: organization
- Location: India
- Website: http://www.iiserpune.ac.in/~cathale
- Repositories: 2
- Profile: https://github.com/CyCelsLab
Self-Organization lab studying the role of collective mechanics and coupling to reaction networks that determine cell shape and division.
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