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.

Proposed by:

Megan Riel-Mehan

Publication

https://www.micropublication.org/journals/biology/micropub-biology-001347

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

An unrelated image from our website showing lots and lots of cells.

Suggested 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

Resources

test software tool

a description for the tool

Materials and methods available:

Dataset

Software Tools

Data and tools made available for use by researchers, that may be of use in pursuing this idea, some available free online, and some available to be purchased or licensed through AICS.