Compare actin filament compression between different fiber-scale simulators
We have previously compared simulations of single actin filament compression at monomer- and fiber-scales using the ReaDDy and Cytosim simulation engines, respectively, under different compression velocities. To better understand how these difference we observed may be specific to the choice of simulators, we proposed running an additional comparison between two simulators at fiber scale.
Interactive visualizations of the previous simulations are available at here.
- actin
- computational modeling
Project proposal:
- Build a MEDYAN model for compression of a single actin filament
- Run simulations at different compression velocities
- Use the subcell-pipeline to align filaments, perform dimensionality reduction, and calculate metrics
Relevant Resources
Preliminary Findings
Fiber-scale simulations of single actin filament compression (using Cytosim) were not able to capture filament supertwist behavior observed with monomer-scale simulations (using ReaDDy).
Figures
an externally linked image
Datasets
Actin compression simulation dataset
This dataset contains simulated data of actin filaments using the monomer-scale model ReaDDy and fiber-scale model Cytosim.
Software Tools
Simularium enables interactive, 3D visualization of the simulation over time. For Simularium files from the Cytosim simulations, see [this…