Files copyright Jakub Koery, University of Glasgow
1. “Discrete_Vimentin_Default.m”
Matlab code (produced in Matlab version R2021a) simulating discrete model for intra-cellular transport using default parameters for vimentin. This single file contains multiple Matlab functions. The main code calls function SolveAtGivenBeadDispl() which solves the discrete problem for increasing value of bead displacement magnitude and outputs the X and Y components of the net force acting on the bead, the exitflag and the solution (x and y coordinates of all network nodes). Function SolveAtGivenBeadDispl() in turn calls function root2d(), in which a vector F of functions dependent on the node coordinates x is defined; SolveAtGivenBeadDispl() then solves the algebraic system F(x)=0. Both functions SolveAtGivenBeadDispl() and root2d() call function FilamentForceLinearOnlyTensile() which outputs the axial force (magnitude, X and Y components) that a filament segment with specified end points experiences.
The code produces the following “.csv” (Excel) files:
a) files saved as ‘XComponentsDisplacement#.csv’ and ‘YComponentsDisplacement#.csv’, where # is the value of bead displacement in microns, store tables containing the x and y coordinates of the solution, respectively. Every row in the tables represents (x or y) coordinates of nodes with a fixed Y coordinate (increasing from the first row to the last), while every column represents nodes with a fixed X coordinate (increasing from the first column to the last) in the initial configuration.
b) file saved as ‘ForceDispl.csv’ contains 4 columns of data:
COL 1: magnitude of bead displacement in microns
COL 2: X-component of the net force acting on the bead in nanonewtons
COL 3: Y-component of the net force acting on the bead in nanonewtons
COL 4: magnitude of the net force acting on the bead in nanonewtons
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2. “Continuum_Vimentin_Default.py”
FEniCS code (produced in FEniCS version 2019.2.0.dev0–) simulating continuum model for intra-cellular transport using default parameters for vimentin (single file). This file solves the continuum problem for increasing value of bead displacement magnitude. This code is based on the documented demo Hyperelasticity (© Copyright FEniCS Project, https://bitbucket.org/fenics-project/) which can be found at
https://fenicsproject.org/olddocs/dolfin/1.6.0/python/demo/documented/hyperelasticity/python/documentation.html
Our code produces the following files:
a) collection ‘DisplVectorField.pvd’ of ‘DisplVectorField#.vtu’ files, where # increases from 000000 to 000010 as the bead displacement increases from 0 to the maximum value. These files store the displacement vector field for increasing bead displacement - this can be visualized (for example) in ParaView.
b) text file saved as ‘ForceDispl.txt’ containing 4 columns of data
COL 1: magnitude of bead displacement in microns
COL 2: X-component of the net force acting on the bead in nanonewtons
COL 3: Y-component of the net force acting on the bead in nanonewtons
COL 4: magnitude of the net force acting on the bead in nanonewtons
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Both the discrete and the continuum code simulate intra-cellular transport using default parameters for vimentin. It is then straight-forward to vary one or more of these parameters and also to specialize the code to actin filaments.