A typical workflow to simulate cytoskeletal systems with Cytosim

TL;DR

This paper presents a detailed workflow for simulating cytoskeletal systems using Cytosim, including setup, configuration, parameter variation, and analysis, facilitating research in cell mechanics.

Contribution

It provides a step-by-step guide for using Cytosim to model cytoskeletal dynamics, making complex simulations accessible without programming skills.

Findings

Systematic variation of crosslinkers affects contractility.

Visual and numerical analysis methods are demonstrated.

Workflow is adaptable to various cytoskeletal problems.

Abstract

Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and the interactions between these elements. Thus, computer simulations can be used to investigate the collective behavior of the system precisely, in a way that is complementary to experiments. Cytosim is an Open Source cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It also offers the possibility to simulate passive crosslinkers, diffusible crosslinkers, nucleators, cutters and discrete versions of the motors that only step on unoccupied lattice sites on a filament. Other objects complement the filaments by offering spherical or more complicated geometry that can be used to represent chromosomes, nucleus or vesicles in the cell. Cytosim offers simple command-line tools for running a simulation and displaying its results, that are versatile and do not require programming skills. In this workflow, step-by-step instructions are given to: i) install the necessary environment on a new computer, ii) configure Cytosim to simulate the contraction of a 2D actomyosin network, iii) produce a visual representation of the system. Next, the system is probed by systematically varying a key parameter: the number of crosslinkers. Finally, the visual representation of the system is complemented by a numerical quantification of contractility to view, in a graph, how contractility depends on the composition of the system. Overall, these different steps constitute a typical workflow that can be applied with few modifications, to tackle many other problems in the cytoskeletal field.