Viscoelasticity analysis of coarse-grained cytoskeletal simulations with Cytosim and Cytocalc

Abstract

Computational modeling has emerged as a powerful approach to studying cytoskeletal dynamics. The simulation software Cytosim provides intuitive yet flexible simulations of filament polymerization, cross-linking, and motor activity. Here, we present Cytocalc, a lightweight Python toolkit designed to streamline and standardize the analysis of Cytosim simulation output, supporting studies of biological functionality and physical properties of cytoskeletal systems. After introducing Cytocalc and validating it, we use it to establish a new workflow for quantifying network viscoelasticity from Cytosim simulations. Specifically, we determine the complex shear modulus of cross-linked networks and quantify how the storage modulus increases with cross-linker density. The cross-linker dependence of the network’s elasticity exhibits two regimes, a scaling regime consistent with elasticity arising from the suppression of thermal bending fluctuations of filaments as well as a much weaker dependence at high cross-linker concentration.