A simple model of active brownian motion used to verify the influence of durotaxis on cellular motility.
Motivational work: https://doi.org/10.1103/PhysRevE.96.010402
Much of the parameters used in this project are well defined in the above paper.
From the working directory open and run any of the three ABP_Durotaxis scripts.
ABP_Durotaxis_Hist.py takes 7 input arguments (with inherent defaults if none are specified):
L: Transition Region Width, default = 3
Dr: Effective Rotational Diffusion Constant, default = 5
ks: soft stiffness parameter, default = 1
kh: hard stiffness parameter, default = 50
vel: cellular velocity, default = 1
nw: number of cells used in simulation, default = 1000
bb: bounding size of system, default = 20
To run, execute in command shell: python ABP_Durotaxis_Hist.py L Dr ks kh vel nw bb (with actual values in place of the input parameters)
The output of this script is a plot of cellular trajectories alongside a histogram of the final horizontal location data
ABP_Durotaxis_MSD.py takes 6 input parameters (w/ inherent defaults):
L: Transition Region Width, default = 3
ks: soft stiffness parameter, default = 1
kh: hard stiffness parameter, default = 50
dt: discrete timeset, default = 0.01
nw: number of cells used in simulation, default = 1000
ns: number of time steps used in simulation, default = 10^6
To run, execute in command shell: python ABP_Durotaxis_MSD.py L ks kh dt nw ns (with actual values in place of input parameters)
The output of this script is a loglog plot of mean square displacement of cells vs time
ABP_Durotaxis_DI.py takes 8 input parameters (w/ inherent defaults):
L: Transition Region Width, default = 3
Dr: Effective Rotational Diffusion Constant, default = 5
ks: soft stiffness parameter, default = 1
kh: hard stiffness parameter, default = 50
vel: cellular velocity, default = 1
nw: number of cells used in simulation, default = 1000
bb: bounding size of system, default = 20
ns: number of time steps, default = 1000
To run, execute in command shell: python ABP_Durotaxis_MSD.py L Dr ks kh vel nw bb ns (w/ actual values in place of input parameters)
The output of this script is a plot of durotaxis index (described in the paper in the background) vs time
The defaults for the parameters above are good starting points for running any of the scripts. There are a few guidelines for choosing parameter values if one wishes to stray from the defaults. L should be on the order of (and less than) bb, ks and kh should remain within an order of magnitude or two of each other (ks < kh), Dr and vel should be on the same order so that the cells exhibit APB. Other than that have fun playing around with the parameters.
For support or questions reach out via nstclair@ucmerced.edu
Thanks to Professor Kinjal Dabiswas of the department of Physics at UC Merced for getting the project off the ground and for the excellent guidance.
[MIT]
Copyright (c) [2020] [Nicholas St. Clair]
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