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Compare actin filament compression between different fiber-scale simulators
Topicsactincomputational modeling
Introduction
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.
Project Proposal
Next steps
- 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
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).
an externally linked image
Relevant Resources
Publication
- https://www.micropublication.org/journals/biology/micropub-biology-001347
Datasets
Software Tools
- test software tool
a description for the tool
- Simularium
3D Agent based modeling.