This git repository contains my work during the summer of 2012. This includes code written in C++ to create a model consisting of a triangular network of springs for networks of actin filaments in the cytoskeleton of cells. Additionally, there are several papers on the topic of modeling cell cytoskeletons and experiments measuring the mechanical properties of cytoskeletons.
There are two simulations set up: first, the static simulation, where the strain is unchanging during the simulation, is in the subdirectory Summer_Internship/testMiles. program uses the conjugate gradient algorithm to minimize the energy of the spring network, which it can then use to calculate the shear modulus of the network. The main file is located in program.cpp and is compiled by the following command:
$ g++ program.cpp -o program
So, to run the program, run
$ ./program
For help, run
$ ./program help
The help file will tell you the correct usage to set the parameters for the simulation.
The second simulation is a dynamic simulation, where the strain applied to the system is sinusoidal. This is located in the Summer_Internship/integrator subdirectory. For each node in the network, the net force is calculated which corresponds to the node's motion. To compile:
$ make integrator.out
To run:
$ ./integrator.out
See the options with
$ ./integrator.out --help
Looking through my code, you might believe that it was written by an unexperienced, amateur coder, and you'd be exactly right. This project has also been a challenge in terms of learning C++ and object-oriented programming. In each subsequent program, I strive to write code that more closely subscribes to the paradigms of makefiles and C++.